diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 1a51bc53..2876c195 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,4 +1,4 @@ -# nf-core/methylseq: Contributing Guidelines +# `nf-core/methylseq`: Contributing Guidelines Hi there! Many thanks for taking an interest in improving nf-core/methylseq. @@ -55,9 +55,9 @@ These tests are run both with the latest available version of `Nextflow` and als :warning: Only in the unlikely and regretful event of a release happening with a bug. -- On your own fork, make a new branch `patch` based on `upstream/master`. +- On your own fork, make a new branch `patch` based on `upstream/main` or `upstream/master`. - Fix the bug, and bump version (X.Y.Z+1). -- A PR should be made on `master` from patch to directly this particular bug. +- Open a pull-request from `patch` to `main`/`master` with the changes. ## Getting help @@ -65,13 +65,13 @@ For further information/help, please consult the [nf-core/methylseq documentatio ## Pipeline contribution conventions -To make the nf-core/methylseq code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. +To make the `nf-core/methylseq` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. ### Adding a new step If you wish to contribute a new step, please use the following coding standards: -1. Define the corresponding input channel into your new process from the expected previous process channel +1. Define the corresponding input channel into your new process from the expected previous process channel. 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new parameters to `nextflow.config` with a default (see below). @@ -84,7 +84,7 @@ If you wish to contribute a new step, please use the following coding standards: ### Default values -Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. +Parameters should be initialised / defined with default values within the `params` scope in `nextflow.config`. Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. diff --git a/.github/actions/nf-test-shard/action.yml b/.github/actions/nf-test-shard/action.yml new file mode 100644 index 00000000..52837a5a --- /dev/null +++ b/.github/actions/nf-test-shard/action.yml @@ -0,0 +1,60 @@ +name: "Get number of shards" +description: "Get the number of nf-test shards for the current CI job" +inputs: + tags: + description: "Tags to pass as argument for nf-test --tag parameter" + required: true + max_shards: + description: "Maximum number of shards allowed" + required: true +outputs: + shard: + description: "Array of shard numbers" + value: ${{ steps.shards.outputs.shard }} + total_shards: + description: "Total number of shards" + value: ${{ steps.shards.outputs.total_shards }} + +runs: + using: "composite" + steps: + - name: Install nf-test + uses: nf-core/setup-nf-test@v1 + with: + version: ${{ env.NFT_VER }} + install-pdiff: true + + - name: Get number of shards + id: shards + shell: bash + run: | + # Run nf-test to get the number of related tests + nftest_output=$(nf-test test --dry-run --changed-since HEAD^ --filter pipeline --tag ${{ inputs.tags }}) + echo "nf-test dry-run output: $nftest_output" + + # Default values for shard and total_shards + shard="[]" + total_shards=0 + + # Check if there are related tests + if echo "$nftest_output" | grep -q 'Nothing to do'; then + echo "No related tests found." + else + # Extract the number of related tests + number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p') + if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then + shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} )) + shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .) + total_shards="$shards_to_run" + else + echo "Unexpected output format. Falling back to default values." + fi + fi + + # Write to GitHub Actions outputs + echo "shard=$shard" >> $GITHUB_OUTPUT + echo "total_shards=$total_shards" >> $GITHUB_OUTPUT + + # Debugging output + echo "Final shard array: $shard" + echo "Total number of shards: $total_shards" diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml new file mode 100644 index 00000000..b5391c7f --- /dev/null +++ b/.github/actions/nf-test/action.yml @@ -0,0 +1,88 @@ +name: "nf-test Action" +description: "Runs nf-test with common setup steps" +inputs: + profile: + description: "Profile to use" + required: true + shard: + description: "Shard number for this CI job" + required: true + total_shards: + description: "Total number of test shards(NOT the total number of matrix jobs)" + required: true + filters: + description: "Filter test cases by specified types (e.g., module, pipeline, workflow or function)" + required: true + tags: + description: "Tags to pass as argument for nf-test --tag parameter" + required: true + +runs: + using: "composite" + steps: + - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4 + with: + distribution: "temurin" + java-version: "17" + + - name: Setup Nextflow + uses: nf-core/setup-nextflow@v2 + with: + version: "${{ env.NXF_VER }}" + + - name: Set up Python + uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 + with: + python-version: "3.11" + + - name: Install nf-test + uses: nf-core/setup-nf-test@v1 + with: + version: "${{ env.NFT_VER }}" + install-pdiff: true + + - name: Setup apptainer + if: contains(inputs.profile, 'singularity') + uses: eWaterCycle/setup-apptainer@main + + - name: Set up Singularity + if: contains(inputs.profile, 'singularity') + shell: bash + run: | + mkdir -p $NXF_SINGULARITY_CACHEDIR + mkdir -p $NXF_SINGULARITY_LIBRARYDIR + + - name: Conda setup + if: ${{inputs.profile == 'conda'}} + uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3 + with: + auto-update-conda: true + conda-solver: libmamba + conda-remove-defaults: true + + - name: Run nf-test + shell: bash + run: | + NFT_WORKDIR=~ \ + nf-test test \ + --ci \ + --shard ${{ inputs.shard }}/${{ inputs.total_shards }} \ + --changed-since HEAD^ \ + --profile=${{ inputs.profile }} \ + --filter ${{ inputs.filters }} \ + --tap=test.tap \ + --verbose \ + --tag ${{ inputs.tags }} + + # TODO If no test.tap, then make one to spoof? + - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 + if: ${{ inputs.path != '' }} + with: + path: >- + test.tap + + - name: Clean up + if: always() + shell: bash + run: | + sudo rm -rf /home/ubuntu/tests/* diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index c68b5424..da4abb43 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,11 +1,12 @@ name: nf-core AWS full size tests -# This workflow is triggered on PRs opened against the master branch. +# This workflow is triggered on PRs opened against the main/master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: pull_request: branches: + - main - master workflow_dispatch: pull_request_review: @@ -21,19 +22,30 @@ jobs: matrix: aligner: ["bismark", "bismark_hisat", "bwameth"] steps: - - uses: octokit/request-action@v2.x + - name: Get PR reviews + uses: octokit/request-action@v2.x if: github.event_name != 'workflow_dispatch' id: check_approvals + continue-on-error: true with: route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100 env: GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - - id: test_variables + + - name: Check for approvals + if: ${{ failure() && github.event_name != 'workflow_dispatch' }} + run: | + echo "No review approvals found. At least 2 approvals are required to run this action automatically." + exit 1 + + - name: Check for enough approvals (>=2) + id: test_variables if: github.event_name != 'workflow_dispatch' run: | JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}' CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length') test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required + - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 with: diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index 65022865..80d5cc35 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -1,15 +1,17 @@ name: nf-core branch protection -# This workflow is triggered on PRs to master branch on the repository -# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` +# This workflow is triggered on PRs to `main`/`master` branch on the repository +# It fails when someone tries to make a PR against the nf-core `main`/`master` branch instead of `dev` on: pull_request_target: - branches: [master] + branches: + - main + - master jobs: test: runs-on: ubuntu-latest steps: - # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches + # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - name: Check PRs if: github.repository == 'nf-core/methylseq' run: | @@ -22,7 +24,7 @@ jobs: uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 with: message: | - ## This PR is against the `master` branch :x: + ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x: * Do not close this PR * Click _Edit_ and change the `base` to `dev` @@ -32,9 +34,9 @@ jobs: Hi @${{ github.event.pull_request.user.login }}, - It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. - The `master` branch on nf-core repositories should always contain code from the latest release. - Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. + It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) ${{github.event.pull_request.base.ref}} branch. + The ${{github.event.pull_request.base.ref}} branch on nf-core repositories should always contain code from the latest release. + Because of this, PRs to ${{github.event.pull_request.base.ref}} are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. Note that even after this, the test will continue to show as failing until you push a new commit. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml deleted file mode 100644 index 21409c6c..00000000 --- a/.github/workflows/ci.yml +++ /dev/null @@ -1,119 +0,0 @@ -name: nf-core CI -# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors -on: - push: - branches: - - dev - pull_request: - release: - types: [published] - workflow_dispatch: - -env: - NXF_ANSI_LOG: false - NFT_VER: "0.9.1" - NFT_WORKDIR: "~" - NFT_DIFF: "pdiff" - NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" - NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity - NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity - -concurrency: - group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" - cancel-in-progress: true - -jobs: - test: - name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})" - # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/methylseq') }}" - runs-on: ubuntu-latest - strategy: - fail-fast: false - matrix: - NXF_VER: - - "24.04.2" - - "latest-everything" - shard: [1, 2, 3, 4, 5] - filter: [pipeline, workflow] - profile: - - "docker" - - "singularity" - test_name: - - "test" - isMaster: - - ${{ github.base_ref == 'master' }} - # Exclude conda and singularity on dev - exclude: - - isMaster: false - profile: "conda" - - isMaster: false - profile: "singularity" - steps: - - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - with: - fetch-depth: 0 - - - name: Set up Nextflow - uses: nf-core/setup-nextflow@v2 - with: - version: "${{ matrix.NXF_VER }}" - - - name: Install pdiff to see diff between nf-test snapshots - run: | - python -m pip install --upgrade pip - pip install pdiff - - - uses: nf-core/setup-nf-test@v1 - with: - version: ${{ env.NFT_VER }} - - - name: Set up Apptainer - if: matrix.profile == 'singularity' - uses: eWaterCycle/setup-apptainer@main - - - name: Set up Singularity - if: matrix.profile == 'singularity' - run: | - mkdir -p $NXF_SINGULARITY_CACHEDIR - mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - - name: Set up Miniconda - if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - with: - miniconda-version: "latest" - auto-update-conda: true - conda-solver: libmamba - channels: conda-forge,bioconda - - - name: Set up Conda - if: matrix.profile == 'conda' - run: | - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH - - - name: Clean up Disk space - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - - name: Run Tests (Shard ${{ matrix.shard }}/${{ strategy.job-total }}) - run: | - nf-test test \ - --ci \ - --shard ${{ matrix.shard }}/${{ strategy.job-total }} \ - --changed-since HEAD^ \ - --profile "+${{ matrix.profile }}" \ - --filter ${{ matrix.filter }} - - - name: Output log on failure - if: failure() - run: | - sudo apt install bat > /dev/null - batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log - - - name: Publish Test Report - uses: mikepenz/action-junit-report@v3 - if: always() # always run even if the previous step fails - with: - report_paths: test.xml diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 713dc3e7..2576cc0c 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -2,7 +2,7 @@ name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually -# - when a PR is opened or reopened to master branch +# - when a PR is opened or reopened to main/master branch # - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev. on: workflow_dispatch: @@ -17,9 +17,11 @@ on: - edited - synchronize branches: + - main - master pull_request_target: branches: + - main - master env: @@ -35,7 +37,7 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" architecture: "x64" @@ -69,7 +71,7 @@ jobs: --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \ --container-cache-utilisation 'amend' \ --download-configuration 'yes' diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index c7ffc80c..ea48f002 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -32,7 +32,7 @@ jobs: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} # Install and run pre-commit - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index a502573c..dbd52d5a 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,10 +14,10 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Set up Python 3.12 - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" @@ -31,12 +31,12 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v2 - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.12" architecture: "x64" @@ -74,7 +74,7 @@ jobs: - name: Upload linting log file artifact if: ${{ always() }} - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: linting-logs path: | diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 42e519bf..0bed96d3 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 + uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml new file mode 100644 index 00000000..3be3cbcb --- /dev/null +++ b/.github/workflows/nf-test-gpu.yml @@ -0,0 +1,119 @@ +name: Run GPU nf-tests +on: + push: + branches: + - dev + pull_request: + release: + types: [published] + workflow_dispatch: + inputs: + runners: + description: "Runners to test on" + type: string + default: "gpu" + +# Cancel if a newer run is started +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver + NFT_VER: "0.9.2" + NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver + NXF_VER: "24.10.2" + +jobs: + get-shards: + runs-on: ubuntu-latest + name: "Get Shards" + outputs: + shard: ${{ steps.set-shards.outputs.shard }} + total_shards: ${{ steps.set-shards.outputs.total_shards }} + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + fetch-depth: 0 + + - name: run nf-test-shard action + id: set-shards + uses: ./.github/actions/nf-test-shard + env: + NFT_VER: ${{ env.NFT_VER }} + with: + tags: "gpu" + max_shards: 2 + + - name: Set outputs + id: set-outputs + run: | + echo "shard=${{ steps.set-shards.outputs.shard }}" >> $GITHUB_ENV + echo "total_shards=${{ steps.set-shards.outputs.total_shards }}" >> $GITHUB_ENV + + nf-test-gpu: + needs: [get-shards] + runs-on: "gpu" + name: "GPU Test | ${{ matrix.profile }} | ${{ matrix.shard }} | ${{ matrix.NXF_VER }} | ${{ matrix.filters }}" + env: + NXF_VER: ${{ matrix.NXF_VER }} + + # Only run on push if this is the nf-core dev branch (merged PRs) + # and number of shards is greater than 0 + if: | + needs.get-shards.outputs.total_shards > 0 && + ( + github.event_name != 'push' || + ( github.event_name == 'push' && github.repository == 'nf-core/methylseq' ) + ) + strategy: + fail-fast: false + matrix: + profile: [docker, singularity] + shard: ${{ fromJson(needs.get-shards.outputs.shard) }} + NXF_VER: + - "24.10.2" + filters: [pipeline] + + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + fetch-depth: 0 + + - name: Run nf-test Action + uses: ./.github/actions/nf-test + with: + profile: ${{ matrix.profile }},gpu + shard: ${{ matrix.shard }} + total_shards: ${{ needs.get-shards.outputs.total_shards }} + filters: ${{ matrix.filters }} + tags: "gpu" + + confirm-pass: + runs-on: ubuntu-latest + needs: [nf-test-gpu] + if: always() + steps: + - name: One or more tests failed + if: ${{ contains(needs.*.result, 'failure') }} + run: exit 1 + + - name: One or more tests cancelled + if: ${{ contains(needs.*.result, 'cancelled') }} + run: exit 1 + + - name: All tests ok + if: ${{ contains(needs.*.result, 'success') }} + run: exit 0 + + - name: debug-print + if: always() + run: | + echo "toJSON(needs) = ${{ toJSON(needs) }}" + echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml new file mode 100644 index 00000000..df9041dd --- /dev/null +++ b/.github/workflows/nf-test.yml @@ -0,0 +1,123 @@ +name: Run nf-tests +on: + push: + branches: + - dev + pull_request: + release: + types: [published] + workflow_dispatch: + inputs: + runners: + description: "Runners to test on" + type: choice + options: + - "ubuntu-latest" + - "self-hosted" + default: "ubuntu-latest" + +# Cancel if a newer run is started +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver + NFT_VER: "0.9.2" + NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver + NXF_VER: "24.10.2" + +jobs: + get-shards: + runs-on: ubuntu-latest + name: "Get Shards" + outputs: + shard: ${{ steps.set-shards.outputs.shard }} + total_shards: ${{ steps.set-shards.outputs.total_shards }} + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + fetch-depth: 0 + + - name: run nf-test-shard action + id: set-shards + uses: ./.github/actions/nf-test-shard + env: + NFT_VER: ${{ env.NFT_VER }} + with: + tags: "cpu" + max_shards: 15 + + - name: Set outputs + id: set-outputs + run: | + echo "shard=${{ steps.set-shards.outputs.shard }}" >> $GITHUB_ENV + echo "total_shards=${{ steps.set-shards.outputs.total_shards }}" >> $GITHUB_ENV + + nf-test: + needs: [get-shards] + runs-on: "ubuntu-latest" + name: "Test | ${{ matrix.profile }} | ${{ matrix.shard }} | ${{ matrix.NXF_VER }} | ${{ matrix.filters }}" + env: + NXF_VER: ${{ matrix.NXF_VER }} + + # Only run on push if this is the nf-core dev branch (merged PRs) + # and number of shards is greater than 0 + if: | + needs.get-shards.outputs.total_shards > 0 && + ( + github.event_name != 'push' || + ( github.event_name == 'push' && github.repository == 'nf-core/methylseq' ) + ) + + strategy: + fail-fast: false + matrix: + profile: [conda, docker, singularity] + shard: ${{ fromJson(needs.get-shards.outputs.shard) }} + NXF_VER: + - "24.10.2" + filters: [pipeline] + + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + fetch-depth: 0 + + - name: Run nf-test Action + uses: ./.github/actions/nf-test + with: + profile: ${{ matrix.profile }} + shard: ${{ matrix.shard }} + total_shards: ${{ needs.get-shards.outputs.total_shards }} + filters: ${{ matrix.filters }} + tags: "cpu" + + confirm-pass: + runs-on: ubuntu-latest + needs: [nf-test] + if: always() + steps: + - name: One or more tests failed + if: ${{ contains(needs.*.result, 'failure') }} + run: exit 1 + + - name: One or more tests cancelled + if: ${{ contains(needs.*.result, 'cancelled') }} + run: exit 1 + + - name: All tests ok + if: ${{ contains(needs.*.result, 'success') }} + run: exit 0 + + - name: debug-print + if: always() + run: | + echo "toJSON(needs) = ${{ toJSON(needs) }}" + echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index c6ba35df..450b1d5e 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -31,7 +31,7 @@ jobs: runs-on: ubuntu-latest steps: - - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5 + - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5 with: python-version: "3.10" - name: Install dependencies diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml index e8aafe44..537529bc 100644 --- a/.github/workflows/template_version_comment.yml +++ b/.github/workflows/template_version_comment.yml @@ -9,7 +9,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4 with: ref: ${{ github.event.pull_request.head.sha }} diff --git a/.gitpod.yml b/.gitpod.yml index 1591998e..5b96c56e 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -12,12 +12,5 @@ tasks: unset JAVA_TOOL_OPTIONS vscode: - extensions: # based on nf-core.nf-core-extensionpack - #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code - - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - - nextflow.nextflow # Nextflow syntax highlighting - - oderwat.indent-rainbow # Highlight indentation level - - streetsidesoftware.code-spell-checker # Spelling checker for source code - - charliermarsh.ruff # Code linter Ruff + extensions: + - nf-core.nf-core-extensionpack # https://github.com/nf-core/vscode-extensionpack diff --git a/.nf-core.yml b/.nf-core.yml index b7f57a7a..66892cca 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -3,9 +3,9 @@ lint: files_exist: - lib/nfcore_external_java_deps.jar - conf/modules.config + - .github/workflows/ci.yml modules_config: false -nf_core_version: 3.0.2 -org_path: +nf_core_version: 3.1.0 repository_type: pipeline template: author: Phil Ewels, Sateesh Peri @@ -16,6 +16,4 @@ template: name: methylseq org: nf-core outdir: . - skip_features: - version: 2.7.1 -update: + version: 3.0.0 diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 00000000..a33b527c --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,3 @@ +{ + "markdown.styles": ["public/vscode_markdown.css"] +} diff --git a/CHANGELOG.md b/CHANGELOG.md index 437105c1..0058b0c2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,34 @@ # nf-core/methylseq +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [v3.0.0](https://github.com/nf-core/methylseq/releases/tag/3.0.0) - [2024-12-16] + +### Bug fixes & refactoring + +- 🐛 fix fasta gunzip output [#462](https://github.com/nf-core/methylseq/pull/457) +- 🐛 fix `bismark/align` not resuming from cache [#461](https://github.com/nf-core/methylseq/pull/457) +- 🐛 uncompressed files won't be saved (https://github.com/nf-core/methylseq/pull/474) +- Updated `conf/modules/samtools_index.config` publishDir configuration to dynamically enable `.bai` file publishing based on whether deduplication is skipped (`--skip_dedup` parameter). This publishing of index files now happens by default as compared to previous, when with `--save_align_intermeds` param. +- 🔄 Updated template to nf-core/tools v3.1.0 [#490](https://github.com/nf-core/methylseq/pull/490) + +> Note: `bwameth/align` module still needs fixing for not resuming from cache. So, its cache has been made **`lenient`** (Minimal input file metadata (name and size only) are included in the cache keys) in its [config](./conf/modules/bwameth_align.config). This strategy provides a workaround for caching invalidation by current `bwameth/align` module requirement to touch the index files before alignment. An issue we hope to have fixed in a release soon. + +### Pipeline Updates + +- 🔧 Install `fastq_align_dedup_bismark` subworkflow from nf-core/subworkflows [#453](https://github.com/nf-core/methylseq/pull/457) +- 🔧 Install `fasta_index_bismark_bwameth` subworkflow from nf-core/subworkflows [#466](https://github.com/nf-core/methylseq/pull/468) +- 🔧 Install `fastq_align_dedup_bwameth` subworkflow from nf-core/subworkflows & introduce `use_gpu` param [#467](https://github.com/nf-core/methylseq/pull/475) +- 🔧 Re-organise & split `conf/modules.config` to `conf/modules/` & `conf/subworkflows/` individual named configs [#459](https://github.com/nf-core/methylseq/pull/469) +- 🔧 `run_preseq` param + skip preseq/lcextrap module by default [#458](https://github.com/nf-core/methylseq/pull/470) +- 🔧 `run_qualimap` param + skip qualimap module by default [#367](https://github.com/nf-core/methylseq/pull/471) +- 🔧 Raised Nextflow version requirement to `24.10.2` +- 🔧 Add CI support for pipeline-level bwameth GPU Tests [#481](https://github.com/nf-core/methylseq/pull/478) +- 🔧 create a test for samplesheet with technical replicates [#477](https://github.com/nf-core/methylseq/pull/486) +- 🔧 Update README, docs/usage and docs/output docs [#487](https://github.com/nf-core/methylseq/pull/489) +- 🔧 Add Bisulfite Sequencing & Three-Base Aligners primer doc [#405](https://github.com/nf-core/methylseq/pull/494) + ## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27] ### Bug fixes & refactoring diff --git a/README.md b/README.md index 00202575..cf30cb9a 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ [![GitHub Actions Linting Status](https://github.com/nf-core/methylseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/methylseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/methylseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1343417-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1343417) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) -[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/) +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.10.2-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -21,17 +21,19 @@ **nf-core/methylseq** is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. -![nf-core/methylseq metro map](docs/images/metromap.png) +![nf-core/methylseq metro map](docs/images/3.0.0_metromap.png) The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker / Singularity containers making installation trivial and results highly reproducible. On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/methylseq/results). +> Read more about **Bisulfite Sequencing & Three-Base Aligners** used in this pipeline [here](./docs/bs-seq-primer.md) + ## Pipeline Summary The pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark) or [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel). -Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`. +Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`. For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html), which implements the baseline tool `bwa-meth` in a performant method using fq2bam (BWA-MEM + GATK) as a backend for processing on GPU. To use this option, include the `--use_gpu` flag along with `--aligner bwameth`. | Step | Bismark workflow | bwa-meth workflow | | -------------------------------------------- | ------------------------ | --------------------- | @@ -44,8 +46,8 @@ Choose between workflows by using `--aligner bismark` (default, uses bowtie2 for | Extract methylation calls | Bismark | MethylDackel | | Sample report | Bismark | - | | Summary Report | Bismark | - | -| Alignment QC | Qualimap | Qualimap | -| Sample complexity | Preseq | Preseq | +| Alignment QC | Qualimap _(optional)_ | Qualimap _(optional)_ | +| Sample complexity | Preseq _(optional)_ | Preseq _(optional)_ | | Project Report | MultiQC | MultiQC | ## Usage @@ -65,9 +67,9 @@ SRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/S Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz, ``` -Each row represents a fastq file (single-end) or a pair of fastq files (paired end). +> Each row represents a fastq file (single-end) or a pair of fastq files (paired end). -Now, you can run the pipeline using: +Now, you can run the pipeline using default parameters as: ```bash nextflow run nf-core/methylseq --input samplesheet.csv --outdir --genome GRCh37 -profile @@ -81,24 +83,20 @@ For more details and further functionality, please refer to the [usage documenta ## Pipeline output To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/methylseq/results) tab on the nf-core website pipeline page. -For more details about the output files and reports, please refer to the -[output documentation](https://nf-co.re/methylseq/output). +For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/methylseq/output). ## Credits -These scripts were originally written for use at the [National Genomics Infrastructure](https://portal.scilifelab.se/genomics/) at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden. - -- Main author: - - Phil Ewels ([@ewels](https://github.com/ewels/)) -- Maintainers: - - Felix Krueger ([@FelixKrueger](https://github.com/FelixKrueger)) - - Sateesh Peri ([@Sateesh_Peri](https://github.com/sateeshperi)) - - Edmund Miller ([@EMiller88](https://github.com/emiller88)) -- Contributors: - - Rickard Hammarén ([@Hammarn](https://github.com/Hammarn/)) - - Alexander Peltzer ([@apeltzer](https://github.com/apeltzer/)) - - Patrick Hüther ([@phue](https://github.com/phue/)) - - Maxime U Garcia ([@maxulysse](https://github.com/maxulysse/)) +nf-core/methylseq was originally written by Phil Ewels ([@ewels](https://github.com/ewels)), and Sateesh Peri ([@sateeshperi](https://github.com/sateeshperi)) is its active maintainer. + +We thank the following people for their extensive assistance in the development of this pipeline: + +- Felix Krueger ([@FelixKrueger](https://github.com/FelixKrueger)) +- Edmund Miller ([@EMiller88](https://github.com/emiller88)) +- Rickard Hammarén ([@Hammarn](https://github.com/Hammarn/)) +- Alexander Peltzer ([@apeltzer](https://github.com/apeltzer/)) +- Patrick Hüther ([@phue](https://github.com/phue/)) +- Maxime U Garcia ([@maxulysse](https://github.com/maxulysse/)) ## Contributions and Support diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f9552e53..a702a0b7 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/methylseq analysis pipeline. For information about how - to interpret these results, please see the documentation. report_section_order: "nf-core-methylseq-methods-description": diff --git a/assets/samplesheet_gpu.csv b/assets/samplesheet_gpu.csv new file mode 100644 index 00000000..fb599e76 --- /dev/null +++ b/assets/samplesheet_gpu.csv @@ -0,0 +1,4 @@ +sample,fastq_1,fastq_2,genome +SRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,, +SRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,, +SRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,, diff --git a/assets/samplesheet_replicates.csv b/assets/samplesheet_replicates.csv new file mode 100644 index 00000000..586f112e --- /dev/null +++ b/assets/samplesheet_replicates.csv @@ -0,0 +1,5 @@ +sample,fastq_1,fastq_2,genome +SRR389222,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,, +SRR389222,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,, +SRR389222,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,, +Ecoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz, diff --git a/conf/base.config b/conf/base.config index 3b0ca369..b3632504 100644 --- a/conf/base.config +++ b/conf/base.config @@ -21,7 +21,7 @@ process { maxErrors = '-1' // Process-specific resource requirements - // NOTE - Please try and re-use the labels below as much as possible. + // NOTE - Please try and reuse the labels below as much as possible. // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. // If possible, it would be nice to keep the same label naming convention when // adding in your local modules too. @@ -59,6 +59,9 @@ process { errorStrategy = 'retry' maxRetries = 2 } + withName: PRESEQ_LCEXTRAP { + errorStrategy = 'ignore' + } withName: BISMARK_ALIGN { time = { 8.d * task.attempt } } diff --git a/modules/nf-core/bismark/align/nextflow.config b/conf/modules/bismark_align.config similarity index 99% rename from modules/nf-core/bismark/align/nextflow.config rename to conf/modules/bismark_align.config index 7e6e83b6..57c74ec9 100644 --- a/modules/nf-core/bismark/align/nextflow.config +++ b/conf/modules/bismark_align.config @@ -35,4 +35,4 @@ process { ] ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/bismark/coverage2cytosine/nextflow.config b/conf/modules/bismark_coverage2cytosine.config similarity index 99% rename from modules/nf-core/bismark/coverage2cytosine/nextflow.config rename to conf/modules/bismark_coverage2cytosine.config index f1a83fb7..8737c561 100644 --- a/modules/nf-core/bismark/coverage2cytosine/nextflow.config +++ b/conf/modules/bismark_coverage2cytosine.config @@ -19,4 +19,4 @@ process { ] ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/bismark/deduplicate/nextflow.config b/conf/modules/bismark_deduplicate.config similarity index 99% rename from modules/nf-core/bismark/deduplicate/nextflow.config rename to conf/modules/bismark_deduplicate.config index b2b51c29..be770f44 100644 --- a/modules/nf-core/bismark/deduplicate/nextflow.config +++ b/conf/modules/bismark_deduplicate.config @@ -9,4 +9,4 @@ process { ] ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/bismark/genomepreparation/nextflow.config b/conf/modules/bismark_genomepreparation.config similarity index 99% rename from modules/nf-core/bismark/genomepreparation/nextflow.config rename to conf/modules/bismark_genomepreparation.config index ed506125..94c3592f 100644 --- a/modules/nf-core/bismark/genomepreparation/nextflow.config +++ b/conf/modules/bismark_genomepreparation.config @@ -11,4 +11,4 @@ process { enabled: params.save_reference ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/bismark/methylationextractor/nextflow.config b/conf/modules/bismark_methylationextractor.config similarity index 99% rename from modules/nf-core/bismark/methylationextractor/nextflow.config rename to conf/modules/bismark_methylationextractor.config index b312885b..a1f69088 100644 --- a/modules/nf-core/bismark/methylationextractor/nextflow.config +++ b/conf/modules/bismark_methylationextractor.config @@ -38,4 +38,4 @@ process { ] ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/bismark/report/nextflow.config b/conf/modules/bismark_report.config similarity index 99% rename from modules/nf-core/bismark/report/nextflow.config rename to conf/modules/bismark_report.config index 597a4684..27e98821 100644 --- a/modules/nf-core/bismark/report/nextflow.config +++ b/conf/modules/bismark_report.config @@ -7,4 +7,4 @@ process { pattern: "*.html" ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/bismark/summary/nextflow.config b/conf/modules/bismark_summary.config similarity index 99% rename from modules/nf-core/bismark/summary/nextflow.config rename to conf/modules/bismark_summary.config index ded23dda..92a5d4c0 100644 --- a/modules/nf-core/bismark/summary/nextflow.config +++ b/conf/modules/bismark_summary.config @@ -7,4 +7,4 @@ process { pattern: "*.{html,txt}" ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/bwameth/align/nextflow.config b/conf/modules/bwameth_align.config similarity index 69% rename from modules/nf-core/bwameth/align/nextflow.config rename to conf/modules/bwameth_align.config index d5cbe70d..bc4ab758 100644 --- a/modules/nf-core/bwameth/align/nextflow.config +++ b/conf/modules/bwameth_align.config @@ -1,5 +1,6 @@ process { withName: BWAMETH_ALIGN { + cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain ext.args = '' publishDir = [ path: { "${params.outdir}/${params.aligner}/alignments" }, @@ -8,4 +9,4 @@ process { enabled: params.save_align_intermeds ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/bwameth/index/nextflow.config b/conf/modules/bwameth_index.config similarity index 99% rename from modules/nf-core/bwameth/index/nextflow.config rename to conf/modules/bwameth_index.config index 92d4e632..74559b06 100644 --- a/modules/nf-core/bwameth/index/nextflow.config +++ b/conf/modules/bwameth_index.config @@ -8,4 +8,4 @@ process { enabled: params.save_reference ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/fastqc/nextflow.config b/conf/modules/fastqc.config similarity index 99% rename from modules/nf-core/fastqc/nextflow.config rename to conf/modules/fastqc.config index 7e31c74d..f611d032 100644 --- a/modules/nf-core/fastqc/nextflow.config +++ b/conf/modules/fastqc.config @@ -14,4 +14,4 @@ process { ] ] } -} \ No newline at end of file +} diff --git a/conf/modules/gunzip.config b/conf/modules/gunzip.config new file mode 100644 index 00000000..3a03a67b --- /dev/null +++ b/conf/modules/gunzip.config @@ -0,0 +1,12 @@ +process { + withName: GUNZIP { + publishDir = [ + [ + path: { "${params.outdir}/gunzip/" }, + mode: params.publish_dir_mode, + pattern: "*.{fa,fasta}", + enabled: false + ] + ] + } +} diff --git a/modules/nf-core/methyldackel/extract/nextflow.config b/conf/modules/methyldackel_extract.config similarity index 99% rename from modules/nf-core/methyldackel/extract/nextflow.config rename to conf/modules/methyldackel_extract.config index f7e24c73..ca274f3d 100644 --- a/modules/nf-core/methyldackel/extract/nextflow.config +++ b/conf/modules/methyldackel_extract.config @@ -19,4 +19,4 @@ process { ] ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/methyldackel/mbias/nextflow.config b/conf/modules/methyldackel_mbias.config similarity index 99% rename from modules/nf-core/methyldackel/mbias/nextflow.config rename to conf/modules/methyldackel_mbias.config index 8ae58f00..3fc655d3 100644 --- a/modules/nf-core/methyldackel/mbias/nextflow.config +++ b/conf/modules/methyldackel_mbias.config @@ -12,4 +12,4 @@ process { ] ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/multiqc/nextflow.config b/conf/modules/multiqc.config similarity index 99% rename from modules/nf-core/multiqc/nextflow.config rename to conf/modules/multiqc.config index 98cf050f..3334a8ec 100644 --- a/modules/nf-core/multiqc/nextflow.config +++ b/conf/modules/multiqc.config @@ -7,4 +7,4 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } -} \ No newline at end of file +} diff --git a/conf/modules/parabricks_fq2bammeth.config b/conf/modules/parabricks_fq2bammeth.config new file mode 100644 index 00000000..71e2596a --- /dev/null +++ b/conf/modules/parabricks_fq2bammeth.config @@ -0,0 +1,12 @@ +process { + withName: PARABRICKS_FQ2BAMMETH { + cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain + ext.args = '--low-memory' + publishDir = [ + path: { "${params.outdir}/${params.aligner}/alignments" }, + pattern: "*.bam", + mode: params.publish_dir_mode, + enabled: params.save_align_intermeds + ] + } +} diff --git a/modules/nf-core/picard/markduplicates/nextflow.config b/conf/modules/picard_markduplicates.config similarity index 99% rename from modules/nf-core/picard/markduplicates/nextflow.config rename to conf/modules/picard_markduplicates.config index 1c3c2ec7..ea2368dc 100644 --- a/modules/nf-core/picard/markduplicates/nextflow.config +++ b/conf/modules/picard_markduplicates.config @@ -15,4 +15,4 @@ process { ] ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/preseq/lcextrap/nextflow.config b/conf/modules/preseq_lcextrap.config similarity index 72% rename from modules/nf-core/preseq/lcextrap/nextflow.config rename to conf/modules/preseq_lcextrap.config index 827ef5ed..efc2a888 100644 --- a/modules/nf-core/preseq/lcextrap/nextflow.config +++ b/conf/modules/preseq_lcextrap.config @@ -5,13 +5,15 @@ process { [ path: { "${params.outdir}/${params.aligner}/preseq" }, mode: params.publish_dir_mode, - pattern: "*.txt" + pattern: "*.txt", + enabled: params.run_preseq ], [ path: { "${params.outdir}/${params.aligner}/preseq/log" }, mode: params.publish_dir_mode, - pattern: "*.log" + pattern: "*.log", + enabled: params.run_preseq ] ] } -} \ No newline at end of file +} diff --git a/conf/modules/qualimap_bamqc.config b/conf/modules/qualimap_bamqc.config new file mode 100644 index 00000000..2cc87871 --- /dev/null +++ b/conf/modules/qualimap_bamqc.config @@ -0,0 +1,16 @@ +process { + withName: QUALIMAP_BAMQC { + ext.args = [ + params.genome.toString().startsWith('GRCh') ? '-gd HUMAN' : '', + params.genome.toString().startsWith('GRCm') ? '-gd MOUSE' : '' + ].join(" ").trim() + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/qualimap/bamqc/" }, + mode: params.publish_dir_mode, + pattern: "*", + enabled: params.run_qualimap + ] + ] + } +} diff --git a/modules/nf-core/samtools/faidx/nextflow.config b/conf/modules/samtools_faidx.config similarity index 99% rename from modules/nf-core/samtools/faidx/nextflow.config rename to conf/modules/samtools_faidx.config index 8b2368a6..26bb23f9 100644 --- a/modules/nf-core/samtools/faidx/nextflow.config +++ b/conf/modules/samtools_faidx.config @@ -8,4 +8,4 @@ process { pattern: "*.fai" ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/samtools/flagstat/nextflow.config b/conf/modules/samtools_flagstat.config similarity index 99% rename from modules/nf-core/samtools/flagstat/nextflow.config rename to conf/modules/samtools_flagstat.config index 2cf4ca87..4b79875c 100644 --- a/modules/nf-core/samtools/flagstat/nextflow.config +++ b/conf/modules/samtools_flagstat.config @@ -8,4 +8,4 @@ process { ] ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/samtools/sort/nextflow.config b/conf/modules/samtools_index.config similarity index 57% rename from modules/nf-core/samtools/sort/nextflow.config rename to conf/modules/samtools_index.config index 1918458c..76cf0fd7 100644 --- a/modules/nf-core/samtools/sort/nextflow.config +++ b/conf/modules/samtools_index.config @@ -1,19 +1,19 @@ process { - withName: SAMTOOLS_SORT { - ext.prefix = { "${meta.id}.sorted" } + withName: SAMTOOLS_INDEX { + ext.prefix = "" publishDir = [ [ path: { "${params.outdir}/${params.aligner}/deduplicated/" }, mode: params.publish_dir_mode, - pattern: "*markdup*.bam", - enabled: params.save_align_intermeds + pattern: "*.bai", + enabled: !params.skip_deduplication ], [ path: { "${params.outdir}/${params.aligner}/alignments/" }, mode: params.publish_dir_mode, - pattern: "*.bam", - enabled: params.save_align_intermeds + pattern: "*.bai", + enabled: params.skip_deduplication ] ] } -} \ No newline at end of file +} diff --git a/conf/modules/samtools_sort.config b/conf/modules/samtools_sort.config new file mode 100644 index 00000000..95c78bd0 --- /dev/null +++ b/conf/modules/samtools_sort.config @@ -0,0 +1,30 @@ +process { + withName: SAMTOOLS_SORT { + ext.prefix = params.skip_deduplication ? { "${meta.id}.sorted" } : { "${meta.id}.deduplicated.sorted" } + publishDir = [ + [ + path: { "${params.outdir}/${params.aligner}/deduplicated/" }, + mode: params.publish_dir_mode, + pattern: "*.deduplicated.sorted.bam" + ], + [ + path: { "${params.outdir}/${params.aligner}/alignments/" }, + mode: params.publish_dir_mode, + pattern: "*.sorted.bam", + enabled: params.skip_deduplication + ], + [ + path: { "${params.outdir}/${params.aligner}/deduplicated/" }, + mode: params.publish_dir_mode, + pattern: "*markdup*.bam", + enabled: params.save_align_intermeds + ], + [ + path: { "${params.outdir}/${params.aligner}/alignments/" }, + mode: params.publish_dir_mode, + pattern: "*.bam", + enabled: params.save_align_intermeds + ] + ] + } +} diff --git a/modules/nf-core/samtools/stats/nextflow.config b/conf/modules/samtools_stats.config similarity index 99% rename from modules/nf-core/samtools/stats/nextflow.config rename to conf/modules/samtools_stats.config index 285e24d7..7574f62f 100644 --- a/modules/nf-core/samtools/stats/nextflow.config +++ b/conf/modules/samtools_stats.config @@ -8,4 +8,4 @@ process { ] ] } -} \ No newline at end of file +} diff --git a/modules/nf-core/trimgalore/nextflow.config b/conf/modules/trimgalore.config similarity index 99% rename from modules/nf-core/trimgalore/nextflow.config rename to conf/modules/trimgalore.config index 6c33f5c4..95b6b1cf 100644 --- a/modules/nf-core/trimgalore/nextflow.config +++ b/conf/modules/trimgalore.config @@ -87,4 +87,4 @@ process { ] ] } -} \ No newline at end of file +} diff --git a/conf/subworkflows/fasta_index_bismark_bwameth.config b/conf/subworkflows/fasta_index_bismark_bwameth.config new file mode 100644 index 00000000..b170b48d --- /dev/null +++ b/conf/subworkflows/fasta_index_bismark_bwameth.config @@ -0,0 +1,4 @@ +includeConfig "../modules/gunzip.config" +includeConfig "../modules/bismark_genomepreparation.config" +includeConfig "../modules/samtools_faidx.config" +includeConfig "../modules/bwameth_index.config" diff --git a/conf/subworkflows/fastq_align_dedup_bismark.config b/conf/subworkflows/fastq_align_dedup_bismark.config new file mode 100644 index 00000000..7531de5a --- /dev/null +++ b/conf/subworkflows/fastq_align_dedup_bismark.config @@ -0,0 +1,8 @@ +includeConfig "../modules/bismark_align.config" +includeConfig "../modules/bismark_deduplicate.config" +includeConfig "../modules/samtools_sort.config" +includeConfig "../modules/samtools_index.config" +includeConfig "../modules/bismark_methylationextractor.config" +includeConfig "../modules/bismark_coverage2cytosine.config" +includeConfig "../modules/bismark_report.config" +includeConfig "../modules/bismark_summary.config" diff --git a/subworkflows/local/bwameth/nextflow.config b/conf/subworkflows/fastq_align_dedup_bwameth.config similarity index 55% rename from subworkflows/local/bwameth/nextflow.config rename to conf/subworkflows/fastq_align_dedup_bwameth.config index 4eff78d7..fec290d8 100644 --- a/subworkflows/local/bwameth/nextflow.config +++ b/conf/subworkflows/fastq_align_dedup_bwameth.config @@ -1,12 +1,12 @@ -includeConfig "../../../modules/nf-core/bwameth/align/nextflow.config" -includeConfig "../../../modules/nf-core/samtools/sort/nextflow.config" - -includeConfig "../../../modules/nf-core/samtools/flagstat/nextflow.config" -includeConfig "../../../modules/nf-core/samtools/stats/nextflow.config" -includeConfig "../../../modules/nf-core/picard/markduplicates/nextflow.config" -includeConfig "../../../modules/nf-core/methyldackel/extract/nextflow.config" -includeConfig "../../../modules/nf-core/methyldackel/mbias/nextflow.config" +includeConfig "../modules/bwameth_align.config" +includeConfig "../modules/parabricks_fq2bammeth.config" +includeConfig "../modules/samtools_sort.config" +includeConfig "../modules/samtools_flagstat.config" +includeConfig "../modules/samtools_stats.config" +includeConfig "../modules/picard_markduplicates.config" +includeConfig "../modules/methyldackel_extract.config" +includeConfig "../modules/methyldackel_mbias.config" process { diff --git a/conf/test.config b/conf/test.config index ebbab61b..244aa906 100644 --- a/conf/test.config +++ b/conf/test.config @@ -18,7 +18,7 @@ params { input = "${projectDir}/assets/samplesheet.csv" // Genome references - fasta = "${params.pipelines_testdata_base_path}/reference/genome.fa" + fasta = "${params.pipelines_testdata_base_path}/reference/genome.fa.gz" fasta_index = "${params.pipelines_testdata_base_path}/reference/genome.fa.fai" } @@ -28,9 +28,5 @@ process { memory: '15.GB', time: '1.h' ] - - withName: PRESEQ_LCEXTRAP { - errorStrategy = 'ignore' - } } diff --git a/docs/bs-seq-primer.md b/docs/bs-seq-primer.md new file mode 100644 index 00000000..f7a04050 --- /dev/null +++ b/docs/bs-seq-primer.md @@ -0,0 +1,132 @@ +# Bisulfite Sequencing & Three-Base Aligners Primer + +[Bisulfite sequencing](https://github.com/nf-core/methylseq) (**BS-seq**) is a widely-used technique to investigate **DNA methylation**, a crucial epigenetic modification that regulates gene expression without altering the DNA sequence. + +## **Principle of Bisulfite Sequencing** + +1. **Bisulfite Treatment**: + + - During bisulfite treatment, **non-methylated cytosines** in DNA are converted to **uracils**, while **methylated cytosines** remain unaffected + - This chemical reaction forms the foundation for distinguishing methylated and unmethylated cytosines + +2. **PCR Amplification**: + + - After bisulfite treatment, the DNA undergoes PCR amplification + - During this step, uracils are converted into **thymines** + - This conversion results in a reduced complexity of the DNA code, introducing computational challenges in downstream analysis + +3. **DNA Strands in Sequencing**: + - For a given genomic locus, bisulfite treatment and PCR amplification produce **four distinct DNA strands**: + - Bisulfite-converted forward strand (OT) + - Reverse complement of OT (CTOT) + - Bisulfite-converted reverse strand (OB) + - Reverse complement of OB (CTOB) + - Depending on library type all four strands may end up in a sequencing library, adding to the complexity of analysis + +## **Applications of Bisulfite Sequencing** + +Bisulfite sequencing is employed to study: + +- **Genome-wide DNA methylation patterns**: Understanding epigenetic regulation of genes +- **Differential methylation**: Investigating differences between different samples (e.g. healthy versus diseased states) +- **Epigenetic inheritance**: Studying methylation changes across generations + +## **Challenges in Mapping Bisulfite-Sequenced Reads** + +Mapping bisulfite-treated sequences to a reference genome presents several computational challenges: + +1. **Reduced DNA Complexity**: + - Due to the conversion of cytosines to thymines, the DNA code becomes less diverse, increasing the likelihood of ambiguous alignments +2. **Multiple DNA Strands**: + - The presence of four possible DNA strands (and their combinations) for each genomic locus increases the alignment search space +3. **Variable Methylation States**: + - Each read can theoretically represent any possible methylation state for a locus, further complicating the alignment process + +## Three-Base Aligners: Bismark and BWA-Meth + +Bisulfite sequencing converts unmethylated cytosines into uracils (later read as thymines during PCR), leading to a DNA code represented predominantly by three bases (A, G, and T). + +Aligning these three-base reads against a standard reference genome is non-trivial, as the original strand identity and methylation state are obscured by the conversion. + +To address these challenges, specialized “three-base aligners” have been developed to accurately map bisulfite-treated reads and infer their original strand context and methylation status. Here, we primarily summarise the aligners used in the nf-core/methylseq pipeline. + +### Bismark ([docs](https://felixkrueger.github.io/Bismark/); [publication](https://pmc.ncbi.nlm.nih.gov/articles/PMC3102221/)) + +- Bismark resolves strand ambiguity by performing up to four parallel alignments +- First, sequencing reads are converted _in silico_ to represent both forward and reverse strand conversions (C-to-T and G-to-A), mirroring fully bisulfite-converted versions of the reference genome +- Each read set is then aligned using Bowtie2 (alternatively HISAT2 or minimap2) against equally converted references; this enables support for indels, local alignments, and bisulfite converted RNA-seq-type or long reads (e.g. EM-seq using Nanopore or Pac Bio reads) +- By comparing these (up-to) four alignments, Bismark identifies each read’s correct strand origin + +This approach allows Bismark to handle directional, PBAT, amplicon, and non-directional libraries robustly and to accurately align reads that represent partially methylated cytosines. + +### BWA-Meth ([docs](https://github.com/brentp/bwa-meth); [publication](https://arxiv.org/abs/1401.1129)) + +- BWA-Meth adapts the BWA-MEM algorithm for bisulfite data, providing efficient, flexible alignments with support for indels, local alignments, and streaming-based workflows. +- By converting reads _in silico_ on the fly, BWA-Meth eliminates the need for intermediate files, reducing temporary storage requirements and simplifying the overall process. +- [Under the hood](https://github.com/brentp/bwa-meth/blob/master/bwameth.py), BWA-Meth maps bisulfite-converted reads to an _in silico_ converted reference. A typical command: + +```bash +python bwameth.py --reference ref.fa A.fq B.fq +``` + +is transparently translated into a command that pipes converted reads directly to bwa mem (or bwa-mem2) without creating temporary files: + +```bash +bwa mem -pCMR ref.fa.bwameth.c2t ' - + - + @@ -30,20 +30,20 @@ - + - + - - + + - + - - - + + + @@ -58,10 +58,8 @@ - - @@ -71,7 +69,7 @@ - + @@ -97,16 +95,19 @@ - + - + + + + diff --git a/docs/images/metromap.png b/docs/images/metromap.png deleted file mode 100644 index 2c3912ad..00000000 Binary files a/docs/images/metromap.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png new file mode 100644 index 00000000..01afbcf8 Binary files /dev/null and b/docs/images/mqc_fastqc_adapter.png differ diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png new file mode 100644 index 00000000..4509bb31 Binary files /dev/null and b/docs/images/mqc_fastqc_counts.png differ diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png new file mode 100644 index 00000000..1ee64e7d Binary files /dev/null and b/docs/images/mqc_fastqc_quality.png differ diff --git a/docs/output.md b/docs/output.md index 4a60d259..21534c6b 100644 --- a/docs/output.md +++ b/docs/output.md @@ -2,9 +2,11 @@ ## Introduction -This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline. +This document describes the output produced by the methylseq pipeline. -Note that nf-core/methylseq contains two workflows - one for Bismark, one for bwa-meth. The results files produced will vary depending on which variant is run. +Most of the plots are taken from the MultiQC report, which summarizes results at the end of the pipeline. + +> NOTE: nf-core/methylseq contains two workflows - one for Bismark, one for bwa-meth. The results files produced will vary depending on which variant is run. The output directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. @@ -18,11 +20,71 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [Deduplication](#deduplication) - Deduplicating reads - [Methylation Extraction](#methylation-extraction) - Calling cytosine methylation steps - [Bismark Reports](#bismark-reports) - Single-sample and summary analysis reports -- [Qualimap](#qualimap) - Tool for genome alignments QC -- [Preseq](#preseq) - Tool for estimating sample complexity +- [Qualimap](#qualimap) - Tool for genome alignments QC [OPTIONAL] +- [Preseq](#preseq) - Tool for estimating sample complexity [OPTIONAL] - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution +### Example output directories of nf-core/methylseq `-test` profile run + +#### Bismark + +``` +bismark/ +├── bismark +│ ├── alignments +│ ├── deduplicated +│ ├── methylation_calls +│ ├── reports +│ └── summary +├── fastqc +│ ├── Ecoli_10K_methylated_1_fastqc.html +│ ├── Ecoli_10K_methylated_2_fastqc.html +│ └── zips +├── multiqc +│ └── bismark +├── pipeline_info +│ ├── execution_report_2024-12-13_05-38-05.html +│ ├── execution_timeline_2024-12-13_05-38-05.html +│ ├── execution_trace_2024-12-13_05-38-05.txt +│ ├── nf_core_methylseq_software_mqc_versions.yml +│ ├── params_2024-12-13_05-38-14.json +│ └── pipeline_dag_2024-12-13_05-38-05.html +└── trimgalore + ├── fastqc + └── logs +``` + +#### bwa-meth + +``` +bwameth/ +├── bwameth +│ ├── alignments +│ └── deduplicated +├── fastqc +│ ├── Ecoli_10K_methylated_1_fastqc.html +│ ├── Ecoli_10K_methylated_2_fastqc.html +│ └── zips +├── methyldackel +│ ├── Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph +│ └── mbias +├── multiqc +│ └── bwameth +├── pipeline_info +│ ├── execution_report_2024-12-13_05-36-34.html +│ ├── execution_timeline_2024-12-13_05-36-34.html +│ ├── execution_trace_2024-12-13_05-36-34.txt +│ ├── nf_core_methylseq_software_mqc_versions.yml +│ ├── params_2024-12-13_05-36-43.json +│ └── pipeline_dag_2024-12-13_05-36-34.html +└── trimgalore + ├── fastqc + └── logs +``` + +### Detailed Output Descriptions + ### FastQC
@@ -54,7 +116,7 @@ The nf-core/methylseq pipeline uses [TrimGalore!](http://www.bioinformatics.babr MultiQC reports the percentage of bases removed by Cutadapt in the _General Statistics_ table, along with a line plot showing where reads were trimmed. -**Output directory: `results/trim_galore`** +**Output directory: `results/trimgalore`** Contains FastQ files with quality and adapter trimmed reads for each sample, along with a log file describing the trimming. @@ -63,7 +125,7 @@ Contains FastQ files with quality and adapter trimmed reads for each sample, alo - **NB:** Only saved if `--save_trimmed` has been specified. - `logs/sample_val_1.fq.gz_trimming_report.txt` - Trimming report (describes which parameters that were used) -- `FastQC/sample_val_1_fastqc.zip` +- `fastQC/sample_val_1_fastqc.zip` - FastQC report for trimmed reads Single-end data will have slightly different file names and only one FastQ file per sample. @@ -72,7 +134,7 @@ Single-end data will have slightly different file names and only one FastQ file Bismark and bwa-meth convert all Cytosines contained within the sequenced reads to Thymine _in-silico_ and then align against a three-letter reference genome. This method avoids methylation-specific alignment bias. The alignment produces a BAM file of genomic alignments. -**Bismark output directory: `results/bismark_alignments/`** +**Bismark output directory: `results/bismark/alignments/`** _Note that bismark can use either use Bowtie2 (default) or HISAT2 as alignment tool and the output file names will not differ between the options._ - `sample.bam` @@ -84,7 +146,7 @@ _Note that bismark can use either use Bowtie2 (default) or HISAT2 as alignment t - Unmapped reads in FastQ format. - Only saved if `--unmapped` specified when running the pipeline. -**bwa-meth output directory: `results/bwa-mem_alignments/`** +**bwa-meth output directory: `results/bwameth/alignments/`** - `sample.bam` - Aligned reads in BAM format. @@ -95,23 +157,23 @@ _Note that bismark can use either use Bowtie2 (default) or HISAT2 as alignment t - `sample.sorted.bam.bai` - Index of sorted BAM file - **NB:** Only saved if `--save_align_intermeds`, `--skip_deduplication` or `--rrbs` is specified when running the pipeline. -- `logs/sample_flagstat.txt` +- `logs/samtools_stats/sample_flagstat.txt` - Summary file describing the number of reads which aligned in different ways. -- `logs/sample_stats.txt` +- `logs/samtools_stats/sample_stats.txt` - Summary file giving lots of metrics about the aligned BAM file. ### Deduplication This step removes alignments with identical mapping position to avoid technical duplication in the results. Note that it is skipped if `--save_align_intermeds`, `--skip_deduplication` or `--rrbs` is specified when running the pipeline. -**Bismark output directory: `results/bismark_deduplicated/`** +**Bismark output directory: `results/bismark/deduplicated/`** - `deduplicated.bam` - BAM file with only unique alignments. - `logs/deduplication_report.txt` - Log file giving summary statistics about deduplication. -**bwa-meth output directory: `results/bwa-mem_markDuplicates/`** +**bwa-meth output directory: `results/bwameth/deduplicated/`** > **NB:** The bwa-meth step doesn't remove duplicate reads from the BAM file, it just labels them. @@ -135,7 +197,7 @@ Filename abbreviations stand for the following reference alignment strands: - `CTOT` - complementary to original top strand - `CTOB` - complementary to original bottom strand -**Bismark output directory: `results/bismark_methylation_calls/`** +**Bismark output directory: `results/bismark/methylation_calls/`** > **NB:** `CTOT` and `CTOB` are not aligned unless `--non_directional` specified. @@ -150,7 +212,7 @@ Filename abbreviations stand for the following reference alignment strands: - `logs/sample_splitting_report.txt` - Log file giving summary statistics about methylation extraction. -**bwa-meth workflow output directory: `results/MethylDackel/`** +**bwa-meth workflow output directory: `results/methyldackel/`** - `sample.bedGraph` - Methylation statuses in [bedGraph](http://genome.ucsc.edu/goldenPath/help/bedgraph.html) format. diff --git a/docs/usage.md b/docs/usage.md index 3e376c1e..aa4c6b25 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -6,7 +6,6 @@ ## Table of contents -- [Table of contents](#table-of-contents) - [Introduction](#introduction) - [Bismark and bwa-meth workflow](#bismark-and-bwa-meth-workflow) - [Running the pipeline](#running-the-pipeline) @@ -15,15 +14,33 @@ ## Introduction -The nf-core/methylseq package is actually two pipelines in one. The default workflow uses [Bismark](http://www.bioinformatics.babraham.ac.uk/projects/bismark/) with [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) as alignment tool: unless specified otherwise, nf-core/methylseq will run this pipeline. +The nf-core/methylseq pipeline provides two distinct workflows for DNA methylation analysis. These workflows support different aligners and cater to a range of computational requirements. -Since bismark v0.21.0 it is also possible to use [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) as alignment tool. To run this workflow, invoke the pipeline with the command line flag `--aligner bismark_hisat`. HISAT2 also supports splice-aware alignment if analysis of RNA is desired (e.g. [SLAMseq](https://science.sciencemag.org/content/360/6390/800) experiments), a file containing a list of known splicesites can be provided with `--known_splices`. +> Read more about **Bisulfite Sequencing & Three-Base Aligners** used in this pipeline [here](./docs/bs-seq-primer.md) -The second workflow uses [BWA-Meth](https://github.com/brentp/bwa-meth) and [MethylDackel](https://github.com/dpryan79/methyldackel) instead of Bismark. To run this workflow, run the pipeline with the command line flag `--aligner bwameth`. +### Workflow: Bismark + +By default, the nf-core/methylseq pipeline uses [Bismark](http://www.bioinformatics.babraham.ac.uk/projects/bismark/) with [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) as the alignment tool. This configuration is optimized for most DNA methylation workflows and will run unless an alternative aligner is specified. + +Starting with Bismark `v0.21.0`, the pipeline also supports [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) as an alternative aligner. To activate this option, use the command-line flag `--aligner bismark_hisat`. + +> HISAT2 offers splice-aware alignment, making it suitable for RNA-based analyses (e.g., [SLAMseq](https://science.sciencemag.org/content/360/6390/800) experiments). For such cases, you can supply a file with known splice sites using the `--known_splices` parameter. + +### Workflow: BWA-Meth + +The second workflow uses [BWA-Meth](https://github.com/brentp/bwa-meth) as the alignment tool and [MethylDackel](https://github.com/dpryan79/methyldackel) for post-processing. + +bwa-meth aligner options: + +- Standard `bwa-meth` (CPU-based): This option can be invoked via `--aligner bwameth` and uses the traditional BWA-Meth aligner and runs on CPU processors. + +- `Parabricks/FQ2BAMMETH` (GPU-based): For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html), which implements the baseline tool `bwa-meth` in a performant method using fq2bam (BWA-MEM + GATK) as a backend for processing on GPU. To use this option, include the `--use_gpu` flag along with `--aligner bwameth`. ## Samplesheet input -You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row as shown in the examples below. +Before running the pipeline, you must create a samplesheet containing information about the samples to be analyzed. Use the appropriate parameter to specify the location of this file. + +The samplesheet must be a comma-separated file (CSV) with four columns and a header row, formatted as shown in the examples below: ```bash --input '[path to samplesheet file]' @@ -35,21 +52,23 @@ sample,fastq_1,fastq_2,genome ### Multiple runs of the same sample -The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: +When a `sample` has been re-sequenced multiple times (e.g., to increase sequencing depth), the sample identifiers must remain the same across all runs. This ensures that the pipeline concatenates the raw reads from all runs before proceeding with downstream analysis. + +Below is an example where the same sample (single-end) has been sequenced across three lanes: ```csv title="samplesheet.csv" sample,fastq_1,fastq_2,genome -SRR389222_sub1,SRR389222_sub1.fastq.gz,, -SRR389222_sub2,SRR389222_sub2.fastq.gz,, -SRR389222_sub3,SRR389222_sub3.fastq.gz,, +SRR389222,SRR389222_sub1.fastq.gz,, +SRR389222,SRR389222_sub2.fastq.gz,, +SRR389222,SRR389222_sub3.fastq.gz,, Ecoli_10K_methylated,Ecoli_10K_methylated_R1.fastq.gz,Ecoli_10K_methylated_R2.fastq.gz, ``` ### Full samplesheet -The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below. +The pipeline automatically detects whether a sample is single- or paired-end based on the information provided in the samplesheet. While additional columns can be included for metadata or other purposes, the first three columns must strictly adhere to the format described in the table below. -A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. +A completed samplesheet containing both single- and paired-end data might look like the example below. In this case, the sheet includes six samples, with `TREATMENT_REP3 `sequenced twice: ```csv title="samplesheet.csv" sample,fastq_1,fastq_2,genome @@ -71,12 +90,30 @@ TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz,, An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. +## Parameters + +Check out the full list of parameters required, available for multiple aligners on [nf-core/methylseq pipeline parameters page](https://nf-co.re/methylseq/3.0.0/parameters/). + +- [Input/output options](https://nf-co.re/methylseq/3.0.0/parameters/#input-output-options) +- [Save intermediate files](https://nf-co.re/methylseq/3.0.0/parameters/#save-intermediate-files) +- [Reference genome options](https://nf-co.re/methylseq/3.0.0/parameters/#reference-genome-options) +- [Alignment options](https://nf-co.re/methylseq/3.0.0/parameters/#alignment-options) +- [Special library types](https://nf-co.re/methylseq/3.0.0/parameters/#special-library-types) +- [Adapter Trimming](https://nf-co.re/methylseq/3.0.0/parameters/#adapter-trimming) +- [Bismark options](https://nf-co.re/methylseq/3.0.0/parameters/#bismark-options) +- [bwa-meth options](https://nf-co.re/methylseq/3.0.0/parameters/#bwa-meth-options) +- [Qualimap Options](https://nf-co.re/methylseq/3.0.0/parameters/#bwa-meth-options) +- [Skip pipeline steps](https://nf-co.re/methylseq/3.0.0/parameters/#skip-pipeline-steps) +- [Run pipeline steps](https://nf-co.re/methylseq/3.0.0/parameters/#Run-pipeline-steps) + +> It is mandatory to provide `--fasta` along with `--bismark_index`/`--bwameth_index` parameters + ## Running the pipeline The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/methylseq --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker +nextflow run nf-core/methylseq --input ./samplesheet.csv --outdir ./results --genome GRCh38 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -94,9 +131,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. -:::warning -Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -::: +> [!WARNING] +> Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). The above pipeline run specified with a params file in yaml format: @@ -115,6 +151,37 @@ genome: 'GRCh37' You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). +### Providing `ext.args` to Tools + +Additional arguments can be appended to a command in a module by specifying them within the module’s custom configuration. The configurations for modules and subworkflows used in the pipeline can be found in `conf/modules` or `conf/subworkflows`. A module’s publishDir path can also be customized in these configurations. + +For example, users working with unfinished genomes containing tens or even hundreds of thousands of scaffolds, contigs, or chromosomes often encounter errors when pre-sorting reads into individual chromosome files. + +These errors are typically caused by the operating system’s limit on the number of file handles that can be open simultaneously (usually 1024; to find out this limit on Linux, use the command: ulimit -a). + +To bypass this limitation, the `--scaffolds` option can be added as an additional `ext.args` in `conf/modules/bismark_methylationextractor.config`. + +This prevents methylation calls from being pre-sorted into individual chromosome files. + +Instead, all input files are temporarily merged into a single file (unless there is only one file), which is then sorted by both chromosome and position using the Unix sort command. + +For a detailed list of different options available, please refer to the official docs of: + +- [Bismark](https://felixkrueger.github.io/Bismark/options/genome_preparation/) +- [bwa-meth](https://github.com/brentp/bwa-meth) + +### Running the `test` profile + +Every nf-core pipeline comes with test data than can be run using `-profile test`. This test profile is useful for testing whether a user's environment is properly setup. + +```bash +nextflow run nf-core/methylseq \ + --input samplesheet.csv \ + --outdir \ + --genome GRCh38 \ + -profile test, +``` + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: @@ -125,23 +192,21 @@ nextflow pull nf-core/methylseq ## Reproducibility -It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. +It is a good idea to specify the pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since. First, go to the [nf-core/methylseq releases page](https://github.com/nf-core/methylseq/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag. This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. -To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. +To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. -:::tip -If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. -::: +> [!TIP] +> If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. ## Core Nextflow arguments -:::note -These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). -::: +> [!NOTE] +> These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen) ### `-profile` @@ -149,16 +214,15 @@ Use this parameter to choose a configuration profile. Profiles can give configur Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. -:::info -We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -::: +> [!IMPORTANT] +> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). +The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. -If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer enviroment. +If `-profile` is not specified, the pipeline will run locally and expect all software to be installed and available on the `PATH`. This is _not_ recommended, since it can lead to different results on different machines dependent on the computer environment. - `test` - A profile with a complete configuration for automated testing @@ -194,13 +258,13 @@ Specify the path to a specific config file (this is a core Nextflow command). Se ### Resource requests -Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the steps in the pipeline, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher requests (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. +Whilst the default requirements set within the pipeline will hopefully work for most people and with most input data, you may find that you want to customise the compute resources that the pipeline requests. Each step in the pipeline has a default set of requirements for number of CPUs, memory and time. For most of the pipeline steps, if the job exits with any of the error codes specified [here](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L18) it will automatically be resubmitted with higher resources request (2 x original, then 3 x original). If it still fails after the third attempt then the pipeline execution is stopped. To change the resource requests, please see the [max resources](https://nf-co.re/docs/usage/configuration#max-resources) and [tuning workflow resources](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources) section of the nf-core website. ### Custom Containers -In some cases you may wish to change which container or conda environment a step of the pipeline uses for a particular tool. By default nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However in some cases the pipeline specified version maybe out of date. +In some cases, you may wish to change the container or conda environment used by a pipeline steps for a particular tool. By default, nf-core pipelines use containers and software from the [biocontainers](https://biocontainers.pro/) or [bioconda](https://bioconda.github.io/) projects. However, in some cases the pipeline specified version maybe out of date. To use a different container from the default container or conda environment specified in a pipeline, please see the [updating tool versions](https://nf-co.re/docs/usage/configuration#updating-tool-versions) section of the nf-core website. @@ -219,38 +283,74 @@ Work dir: Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` ``` -#### For beginners +#### Resource Limits + +In addition to the executor, you may find that pipeline runs occasionally fail due to a particular step of the pipeline requesting more resources than you have on your system. + +To avoid these failures, you can tell Nextflow to set a cap pipeline-step resource requests against a list called `resourceLimits` specified in Nextflow config file. These should represent the maximum possible resources of a machine or node. + +Specify the maximum resources that can be used (cpus, memory, time) for all processes by default or for a specific process using `withName` or `withLabel` selectors as shown below: -A first step to bypass this error, you could try to increase the amount of CPUs, memory, and time for the whole pipeline. Therefor you can try to increase the resource for the parameters `--max_cpus`, `--max_memory`, and `--max_time`. Based on the error above, you have to increase the amount of memory. Therefore you can go to the [parameter documentation of rnaseq](https://nf-co.re/rnaseq/3.9/parameters) and scroll down to the `show hidden parameter` button to get the default value for `--max_memory`. In this case 128GB, you than can try to run your pipeline again with `--max_memory 200GB -resume` to skip all process, that were already calculated. If you can not increase the resource of the complete pipeline, you can try to adapt the resource for a single process as mentioned below. +> Global resource limits + +``` +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} +``` + +> Process-specific resource limits + +``` +process { + withName: 'BISMARK_ALIGN' { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] + } +} +``` #### Advanced option on process level -To bypass this error you would need to find exactly which resources are set by the `STAR_ALIGN` process. The quickest way is to search for `process STAR_ALIGN` in the [nf-core/rnaseq Github repo](https://github.com/nf-core/rnaseq/search?q=process+STAR_ALIGN). -We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/star/align/main.nf`. -If you click on the link to that file you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/modules/nf-core/software/star/align/main.nf#L9). -The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organise workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. -The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/rnaseq/blob/4c27ef5610c87db00c3c5a3eed10b1d161abf575/conf/base.config#L33-L37) which in this case is defined as 72GB. -Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `STAR_ALIGN` process failure by creating a custom config file that sets at least 72GB of memory, in this case increased to 100GB. +To find out exactly what resources have been set for a process, for example., the `BISMARK_ALIGN` process. Navigate to the [BISMARK_ALIGN](../modules/nf-core/bismark/align/main.nf) module used in the workflow. + +> We have standardised the structure of Nextflow DSL2 pipelines such that all module files will be present in the `modules/` directory and so, based on the search results, the file we want is `modules/nf-core/bismark/align/main.nf`. + +In the module `main.nf`, you will notice that there is a `label` directive at the top of the module that is set to [`label process_high`](https://github.com/nf-core/modules/blob/9a19690b0a3fae05fa1a6ad90a0720d681429e31/modules/nf-core/bismark/align/main.nf#L3). + +The [Nextflow `label`](https://www.nextflow.io/docs/latest/process.html#label) directive allows us to organize workflow processes in separate groups which can be referenced in a configuration file to select and configure subset of processes having similar computing requirements. + +The default values for the `process_high` label are set in the pipeline's [`base.config`](https://github.com/nf-core/methylseq/blob/master/conf/base.config) which in this case is defined as `72.GB`. + +Providing you haven't set any other standard nf-core parameters to **cap** the [maximum resources](https://nf-co.re/usage/configuration#max-resources) used by the pipeline then we can try and bypass the `BISMARK_ALIGN` process failure by creating a custom config file that sets at least `72.GB` of memory, in this case increased to `100.GB`. + The custom config below can then be provided to the pipeline via the [`-c`](#-c) parameter as highlighted in previous sections. ```nextflow process { - withName: bismark_align { - memory = 32.GB + withName: 'BISMARK_ALIGN' { + memory = 100.GB } } ``` -> **NB:** We specify the full process name i.e. `NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN` in the config file because this takes priority over the short name (`STAR_ALIGN`) and allows existing configuration using the full process name to be correctly overridden. -> -> If you get a warning suggesting that the process selector isn't recognised check that the process name has been specified correctly. - ### Updating containers (advanced users) -The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon everytime a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`. +The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. + +If for some reason you need to use a different version of a particular tool with the pipeline then you just need to identify the `process` name and override the Nextflow `container` definition for that process using the `withName` declaration. For example, in the [nf-core/viralrecon](https://nf-co.re/viralrecon) pipeline a tool called [Pangolin](https://github.com/cov-lineages/pangolin) has been used during the COVID-19 pandemic to assign lineages to SARS-CoV-2 genome sequenced samples. Given that the lineage assignments change quite frequently it doesn't make sense to re-release the nf-core/viralrecon every time a new version of Pangolin has been released. However, you can override the default container used by the pipeline by creating a custom config file and passing it as a command-line argument via `-c custom.config`. 1. Check the default version used by the pipeline in the module file for [Pangolin](https://github.com/nf-core/viralrecon/blob/a85d5969f9025409e3618d6c280ef15ce417df65/modules/nf-core/software/pangolin/main.nf#L14-L19) + 2. Find the latest version of the Biocontainer available on [Quay.io](https://quay.io/repository/biocontainers/pangolin?tag=latest&tab=tags) + 3. Create the custom config accordingly: - For Docker: diff --git a/main.nf b/main.nf index 5c1056c8..77c8ef37 100644 --- a/main.nf +++ b/main.nf @@ -15,11 +15,11 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { METHYLSEQ } from './workflows/methylseq/' -include { PREPARE_GENOME } from './subworkflows/local/prepare_genome/' -include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_methylseq_pipeline' -include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_methylseq_pipeline' -include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_methylseq_pipeline' +include { FASTA_INDEX_BISMARK_BWAMETH } from './subworkflows/nf-core/fasta_index_bismark_bwameth/main' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_methylseq_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_methylseq_pipeline' +include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_methylseq_pipeline' +include { METHYLSEQ } from './workflows/methylseq/' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -52,13 +52,13 @@ workflow NFCORE_METHYLSEQ { // // SUBWORKFLOW: Prepare any required reference genome indices // - PREPARE_GENOME( + FASTA_INDEX_BISMARK_BWAMETH( params.fasta, params.fasta_index, params.bismark_index, params.bwameth_index, ) - ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions) + ch_versions = ch_versions.mix(FASTA_INDEX_BISMARK_BWAMETH.out.versions) // // WORKFLOW: Run pipeline @@ -67,14 +67,16 @@ workflow NFCORE_METHYLSEQ { METHYLSEQ ( samplesheet, ch_versions, - PREPARE_GENOME.out.fasta, - PREPARE_GENOME.out.fasta_index, - PREPARE_GENOME.out.bismark_index, - PREPARE_GENOME.out.bwameth_index, + FASTA_INDEX_BISMARK_BWAMETH.out.fasta, + FASTA_INDEX_BISMARK_BWAMETH.out.fasta_index, + FASTA_INDEX_BISMARK_BWAMETH.out.bismark_index, + FASTA_INDEX_BISMARK_BWAMETH.out.bwameth_index, ) + ch_versions = ch_versions.mix(METHYLSEQ.out.versions) + emit: - multiqc_report = METHYLSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html - versions = ch_versions // channel: [version1, version2, ...] + multiqc_report = METHYLSEQ.out.multiqc_report // channel: [ path(multiqc_report.html ) ] + versions = ch_versions // channel: [ path(versions.yml) ] } /* diff --git a/modules.json b/modules.json index 0174a44b..7491ed94 100644 --- a/modules.json +++ b/modules.json @@ -7,48 +7,48 @@ "nf-core": { "bismark/align": { "branch": "master", - "git_sha": "dfd89399e3c6e2422c4cdcf0aaa8cf2393dc51c9", - "installed_by": ["modules"] + "git_sha": "9a1e8bb6a5d205cf7807dcefca872a3314b2f3e6", + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "bismark/coverage2cytosine": { "branch": "master", - "git_sha": "430bcb24e43dabcafb5174c955300730e5ad23f7", - "installed_by": ["modules"] + "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03", + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "bismark/deduplicate": { "branch": "master", - "git_sha": "0755c617637d21b2c290b26d225debe3070aa109", - "installed_by": ["modules"] + "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03", + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "bismark/genomepreparation": { "branch": "master", - "git_sha": "3ab4739901f600a16ede0f491abfb6bf5d993cb2", - "installed_by": ["modules"] + "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03", + "installed_by": ["fasta_index_bismark_bwameth", "modules"] }, "bismark/methylationextractor": { "branch": "master", - "git_sha": "0755c617637d21b2c290b26d225debe3070aa109", - "installed_by": ["modules"] + "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03", + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "bismark/report": { "branch": "master", - "git_sha": "0755c617637d21b2c290b26d225debe3070aa109", - "installed_by": ["modules"] + "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03", + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "bismark/summary": { "branch": "master", "git_sha": "dfd89399e3c6e2422c4cdcf0aaa8cf2393dc51c9", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bismark", "modules"] }, "bwameth/align": { "branch": "master", - "git_sha": "dfd89399e3c6e2422c4cdcf0aaa8cf2393dc51c9", - "installed_by": ["modules"] + "git_sha": "2edb63067971fb906749e96bf22b23a4ec892a62", + "installed_by": ["fastq_align_dedup_bwameth", "modules"] }, "bwameth/index": { "branch": "master", "git_sha": "a716d10039f9728f2674f45c33a95b605851ea50", - "installed_by": ["modules"] + "installed_by": ["fasta_index_bismark_bwameth", "modules"] }, "cat/fastq": { "branch": "master", @@ -57,33 +57,38 @@ }, "fastqc": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164", "installed_by": ["modules"] }, "gunzip": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": ["fasta_index_bismark_bwameth", "modules"] }, "methyldackel/extract": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bwameth", "modules"] }, "methyldackel/mbias": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bwameth", "modules"] }, "multiqc": { "branch": "master", "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", "installed_by": ["modules"] }, + "parabricks/fq2bammeth": { + "branch": "master", + "git_sha": "2edb63067971fb906749e96bf22b23a4ec892a62", + "installed_by": ["fastq_align_dedup_bwameth"] + }, "picard/markduplicates": { "branch": "master", "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bwameth", "modules"] }, "preseq/lcextrap": { "branch": "master", @@ -103,55 +108,70 @@ "samtools/faidx": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": ["fasta_index_bismark_bwameth", "modules"] }, "samtools/flagstat": { "branch": "master", - "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540", + "installed_by": ["fastq_align_dedup_bwameth", "modules"] }, "samtools/index": { "branch": "master", "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bismark", "fastq_align_dedup_bwameth", "modules"] }, "samtools/sort": { "branch": "master", "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b", - "installed_by": ["modules"] + "installed_by": ["fastq_align_dedup_bismark", "fastq_align_dedup_bwameth", "modules"] }, "samtools/stats": { "branch": "master", - "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", - "installed_by": ["modules"] + "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540", + "installed_by": ["fastq_align_dedup_bwameth", "modules"] }, "trimgalore": { "branch": "master", - "git_sha": "8c5eeedd45e295fc9a4f164631da6a8b37e6b9c6", + "git_sha": "4c2d06a5e79abf08ba7f04c58e39c7dad75f094d", "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", - "installed_by": ["modules"] + "installed_by": ["fasta_index_bismark_bwameth", "modules"] } } }, "subworkflows": { "nf-core": { + "fasta_index_bismark_bwameth": { + "branch": "master", + "git_sha": "e24c9731daae27a4cd0b072f2e50cc8401a492db", + "installed_by": ["subworkflows"] + }, + "fastq_align_dedup_bismark": { + "branch": "master", + "git_sha": "af84433c2e619cf28e026d4140b1b8763ae3690b", + "installed_by": ["subworkflows"] + }, + "fastq_align_dedup_bwameth": { + "branch": "master", + "git_sha": "bd5f75ccaf2345269810e66e85de8a70e4de8764", + "installed_by": ["subworkflows"] + }, "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", + "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", + "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", + "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index 1de78f32..4aaa1be2 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -9,7 +9,7 @@ process BISMARK_ALIGN { input: tuple val(meta), path(reads) - tuple val(meta2), path(fasta) + tuple val(meta2), path(fasta, stageAs: 'tmp/*') // This change mounts as directory containing the FASTA file to prevent nested symlinks tuple val(meta3), path(index) output: @@ -45,7 +45,7 @@ process BISMARK_ALIGN { // Check that we have enough memory try { - def tmem = (task.memory as nextflow.util.MemoryUnit).toBytes() + def tmem = (task.memory as MemoryUnit).toBytes() def mcore = (tmem / mem_per_multicore) as int ccore = Math.min(ccore, mcore) } catch (all) { @@ -56,13 +56,11 @@ process BISMARK_ALIGN { } } """ - ln -sf \$(readlink $fasta) $index/$fasta - bismark \\ - $fastq \\ - --genome $index \\ + ${fastq} \\ + --genome ${index} \\ --bam \\ - $args + ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bismark/align/tests/main.nf.test b/modules/nf-core/bismark/align/tests/main.nf.test index 059057d3..144c1c98 100644 --- a/modules/nf-core/bismark/align/tests/main.nf.test +++ b/modules/nf-core/bismark/align/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process BISMARK_ALIGN" script "../main.nf" process "BISMARK_ALIGN" + config './nextflow.config' tag "modules" tag "modules_nfcore" @@ -16,16 +17,15 @@ nextflow_process { process { """ input[0] = Channel.of([ - [ id:'test' ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) """ } } } - test("bowtie2 single-end / sarscov2 genome [fasta]") { - config './nextflow.config' + test("bowtie2 | single-end | sarscov2 genome [fasta]") { when { params { @@ -36,8 +36,11 @@ nextflow_process { input[0] = Channel.of([ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) - ]) - input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + ]) + input[1] = Channel.of([ + [ id:'sarscov2'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) input[2] = BISMARK_GENOMEPREPARATION.out.index """ } @@ -47,8 +50,12 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.bam.collect { bam(it[1]).getReadsMD5() }, - file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), + process.out.bam.collect { meta, bamfile -> + bam(bamfile).getReadsMD5() + }, + process.out.report.collect { meta, report -> + file(report).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009") + }, process.out.unmapped, process.out.versions ).match() @@ -57,8 +64,7 @@ nextflow_process { } } - test("bowtie2 paired-end / sarscov2 genome [fasta]") { - config './nextflow.config' + test("bowtie2 | paired-end | sarscov2 genome [fasta]") { when { params { @@ -72,8 +78,11 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) ] - ]) - input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + ]) + input[1] = Channel.of([ + [ id:'sarscov2'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) input[2] = BISMARK_GENOMEPREPARATION.out.index """ } @@ -83,8 +92,16 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.bam.collect { bam(it[1][0]).getReadsMD5() }, - file(process.out.report[0][1][0]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), + process.out.bam.collect { meta, bamfiles -> + bamfiles.collect { bamfile -> + bam(bamfile).getReadsMD5() + } + }, + process.out.report.collect { meta, reports -> + reports.collect { report -> + file(report).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009") + } + }, process.out.unmapped, process.out.versions ).match() @@ -93,8 +110,7 @@ nextflow_process { } } - test("hisat2 single-end / sarscov2 genome [fasta]") { - config './nextflow.config' + test("hisat2 | single-end | sarscov2 genome [fasta]") { when { params { @@ -105,8 +121,11 @@ nextflow_process { input[0] = Channel.of([ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) - ]) - input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + ]) + input[1] = Channel.of([ + [ id:'sarscov2'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) input[2] = BISMARK_GENOMEPREPARATION.out.index """ } @@ -116,8 +135,12 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.bam.collect { bam(it[1]).getReadsMD5() }, - file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), + process.out.bam.collect { meta, bamfile -> + bam(bamfile).getReadsMD5() + }, + process.out.report.collect { meta, report -> + file(report).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009") + }, process.out.unmapped, process.out.versions ).match() @@ -126,8 +149,7 @@ nextflow_process { } } - test("hisat2 paired-end / sarscov2 genome [fasta]") { - config './nextflow.config' + test("hisat2 | paired-end | sarscov2 genome [fasta]") { when { params { @@ -141,8 +163,11 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) ] - ]) - input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + ]) + input[1] = Channel.of([ + [ id:'sarscov2'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) input[2] = BISMARK_GENOMEPREPARATION.out.index """ } @@ -152,8 +177,16 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.bam.collect { bam(it[1][0]).getReadsMD5() }, - file(process.out.report[0][1][0]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), + process.out.bam.collect { meta, bamfiles -> + bamfiles.collect { bamfile -> + bam(bamfile).getReadsMD5() + } + }, + process.out.report.collect { meta, reports -> + reports.collect { report -> + file(report).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009") + } + }, process.out.unmapped, process.out.versions ).match() @@ -162,8 +195,7 @@ nextflow_process { } } - test("minimap2 single-end / sarscov2 genome [fasta]") { - config './nextflow.config' + test("minimap2 | single-end | sarscov2 genome [fasta]") { when { params { @@ -174,8 +206,53 @@ nextflow_process { input[0] = Channel.of([ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) - ]) - input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + ]) + input[1] = Channel.of([ + [ id:'sarscov2'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.bam.collect { meta, bamfile -> + bam(bamfile).getReadsMD5() + }, + process.out.report.collect { meta, report -> + file(report).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009") + }, + process.out.unmapped, + process.out.versions + ).match() + } + ) + } + } + + test("minimap2 | paired-end | sarscov2 genome [fasta]") { + + when { + params { + bismark_args = '--minimap2' + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'sarscov2'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) input[2] = BISMARK_GENOMEPREPARATION.out.index """ } @@ -185,8 +262,16 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.bam.collect { bam(it[1]).getReadsMD5() }, - file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5047"), + process.out.bam.collect { meta, bamfiles -> + bamfiles.collect { bamfile -> + bam(bamfile).getReadsMD5() + } + }, + process.out.report.collect { meta, reports -> + reports.collect { report -> + file(report).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009") + } + }, process.out.unmapped, process.out.versions ).match() @@ -194,4 +279,38 @@ nextflow_process { ) } } + + test("minimap2 | paired-end | sarscov2 genome [fasta] | stub") { + options "-stub" + + when { + params { + bismark_args = '--minimap2' + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'sarscov2'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + } } diff --git a/modules/nf-core/bismark/align/tests/main.nf.test.snap b/modules/nf-core/bismark/align/tests/main.nf.test.snap index 3842cd6d..5dfdfbfe 100644 --- a/modules/nf-core/bismark/align/tests/main.nf.test.snap +++ b/modules/nf-core/bismark/align/tests/main.nf.test.snap @@ -1,10 +1,12 @@ { - "bowtie2 paired-end / sarscov2 genome [fasta]": { + "minimap2 | single-end | sarscov2 genome [fasta]": { "content": [ [ - "936c0d5ce713130113e99e09a5b53afd" + "d354e6c6d6a06e36630590de8f27031a" + ], + [ + false ], - true, [ ], @@ -13,17 +15,25 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-13T17:35:23.192447327" + "timestamp": "2024-11-20T07:06:10.385317868" }, - "hisat2 paired-end / sarscov2 genome [fasta]": { + "hisat2 | paired-end | sarscov2 genome [fasta]": { "content": [ [ - "936c0d5ce713130113e99e09a5b53afd" + [ + "936c0d5ce713130113e99e09a5b53afd", + "5636a8adfbdd353026686e888996a47c" + ] + ], + [ + [ + true, + false + ] ], - true, [ ], @@ -32,17 +42,25 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-13T17:36:10.145541495" + "timestamp": "2024-11-20T07:12:14.540260123" }, - "minimap2 single-end / sarscov2 genome [fasta]": { + "bowtie2 | paired-end | sarscov2 genome [fasta]": { "content": [ [ - "d354e6c6d6a06e36630590de8f27031a" + [ + "936c0d5ce713130113e99e09a5b53afd", + "5636a8adfbdd353026686e888996a47c" + ] + ], + [ + [ + true, + false + ] ], - true, [ ], @@ -51,17 +69,19 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-13T17:36:32.094369612" + "timestamp": "2024-11-20T07:04:42.515898978" }, - "bowtie2 single-end / sarscov2 genome [fasta]": { + "bowtie2 | single-end | sarscov2 genome [fasta]": { "content": [ [ "936c0d5ce713130113e99e09a5b53afd" ], - true, + [ + true + ], [ ], @@ -70,17 +90,46 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-13T17:34:58.431003479" + "timestamp": "2024-11-20T06:50:16.487384391" }, - "hisat2 single-end / sarscov2 genome [fasta]": { + "hisat2 | single-end | sarscov2 genome [fasta]": { "content": [ [ "936c0d5ce713130113e99e09a5b53afd" ], - true, + [ + true + ], + [ + + ], + [ + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-11-20T06:51:06.34107409" + }, + "minimap2 | paired-end | sarscov2 genome [fasta]": { + "content": [ + [ + [ + "d354e6c6d6a06e36630590de8f27031a", + "109762b26674693cd29fddb18da0d1fa" + ] + ], + [ + [ + false, + false + ] + ], [ ], @@ -89,9 +138,68 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-11-20T07:12:59.868431446" + }, + "minimap2 | paired-end | sarscov2 genome [fasta] | stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" + ], + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "report": [ + [ + { + "id": "test", + "single_end": true + }, + "test.report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "unmapped": [ + + ], + "versions": [ + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-13T17:35:45.557280528" + "timestamp": "2024-11-20T07:16:21.454058443" } } \ No newline at end of file diff --git a/modules/nf-core/bismark/coverage2cytosine/main.nf b/modules/nf-core/bismark/coverage2cytosine/main.nf index fe65c658..9e1be2a1 100644 --- a/modules/nf-core/bismark/coverage2cytosine/main.nf +++ b/modules/nf-core/bismark/coverage2cytosine/main.nf @@ -9,7 +9,7 @@ process BISMARK_COVERAGE2CYTOSINE { input: tuple val(meta), path(coverage_file) - tuple val(meta2), path(fasta) + tuple val(meta2), path(fasta, stageAs: 'tmp/*') // This change mounts as directory containing the FASTA file to prevent nested symlinks tuple val(meta3), path(index) output: @@ -25,16 +25,12 @@ process BISMARK_COVERAGE2CYTOSINE { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - if [ ! -f $index/$fasta ]; then - ln -s \$(readlink $fasta) $index/$fasta; - fi - coverage2cytosine \\ - $coverage_file \\ - --genome $index \\ + ${coverage_file} \\ + --genome ${index} \\ --output ${prefix} \\ --gzip \\ - $args + ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf index 2da9312c..394bf951 100644 --- a/modules/nf-core/bismark/deduplicate/main.nf +++ b/modules/nf-core/bismark/deduplicate/main.nf @@ -24,9 +24,9 @@ process BISMARK_DEDUPLICATE { def seqtype = meta.single_end ? '-s' : '-p' """ deduplicate_bismark \\ - $args \\ - $seqtype \\ - --bam $bam + ${args} \\ + ${seqtype} \\ + --bam ${bam} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index c94e9fec..eea0cfb9 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -21,11 +21,9 @@ process BISMARK_GENOMEPREPARATION { def args = task.ext.args ?: '' """ bismark_genome_preparation \\ - $args \\ + ${args} \\ BismarkIndex - rm $fasta - cat <<-END_VERSIONS > versions.yml "${task.process}": bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') diff --git a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap index d56b414d..6feb91ac 100644 --- a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap +++ b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap @@ -102,7 +102,8 @@ "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6", "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59" ] - ] + ], + "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6" ] ] ], @@ -134,7 +135,8 @@ "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6", "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59" ] - ] + ], + "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6" ] ] ], @@ -144,9 +146,9 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-13T08:26:20.352083082" + "timestamp": "2024-11-25T15:32:55.125985002" } } \ No newline at end of file diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf index 3a71d35d..dce78555 100644 --- a/modules/nf-core/bismark/methylationextractor/main.nf +++ b/modules/nf-core/bismark/methylationextractor/main.nf @@ -36,13 +36,13 @@ process BISMARK_METHYLATIONEXTRACTOR { def seqtype = meta.single_end ? '-s' : '-p' """ bismark_methylation_extractor \\ - $bam \\ + ${bam} \\ --bedGraph \\ --counts \\ --gzip \\ --report \\ - $seqtype \\ - $args + ${seqtype} \\ + ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf index e68ee8e5..732e85d3 100644 --- a/modules/nf-core/bismark/report/main.nf +++ b/modules/nf-core/bismark/report/main.nf @@ -20,7 +20,7 @@ process BISMARK_REPORT { script: def args = task.ext.args ?: '' """ - bismark2report $args + bismark2report ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test b/modules/nf-core/bwameth/align/tests/main.nf.test index 37dd4ad2..87195e0c 100644 --- a/modules/nf-core/bwameth/align/tests/main.nf.test +++ b/modules/nf-core/bwameth/align/tests/main.nf.test @@ -117,5 +117,4 @@ nextflow_process { ) } } - } diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d8989f48..752c3a10 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -24,7 +24,7 @@ process FASTQC { // Make list of old name and new name pairs to use for renaming in the bash while loop def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') + def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ') // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index 4827da7a..2b2e62b8 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -11,6 +11,7 @@ tools: FastQC gives general quality metrics about your reads. It provides information about the quality score distribution across your reads, the per base sequence content (%A/C/G/T). + You get information about adapter contamination and other overrepresented sequences. homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ diff --git a/modules/nf-core/gunzip/tests/main.nf.test.snap b/modules/nf-core/gunzip/tests/main.nf.test.snap index 069967e7..8e6df73a 100644 --- a/modules/nf-core/gunzip/tests/main.nf.test.snap +++ b/modules/nf-core/gunzip/tests/main.nf.test.snap @@ -28,7 +28,7 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.10.2" }, "timestamp": "2024-06-25T11:35:10.861293" }, @@ -61,7 +61,7 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.10.2" }, "timestamp": "2024-06-25T11:35:05.857145" }, @@ -94,7 +94,7 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.10.2" }, "timestamp": "2023-10-17T15:35:37.690477896" }, @@ -127,7 +127,7 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.10.2" }, "timestamp": "2024-06-25T11:33:32.921739" } diff --git a/modules/nf-core/parabricks/fq2bammeth/main.nf b/modules/nf-core/parabricks/fq2bammeth/main.nf new file mode 100644 index 00000000..eb7ae685 --- /dev/null +++ b/modules/nf-core/parabricks/fq2bammeth/main.nf @@ -0,0 +1,70 @@ +process PARABRICKS_FQ2BAMMETH { + tag "$meta.id" + label 'process_high' + label 'process_gpu' + + container "nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1" + + input: + tuple val(meta), path(reads) + tuple val(meta2), path(fasta) + tuple val(meta3), path(index) + path(known_sites) + + output: + tuple val(meta), path("*.bam") , emit: bam + tuple val(meta), path("*.bai") , emit: bai + path("qc_metrics") , emit: qc_metrics, optional:true + path("*.table") , emit: bqsr_table, optional:true + path("duplicate-metrics.txt") , emit: duplicate_metrics, optional:true + path("versions.yml") , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead." + } + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def in_fq_command = meta.single_end ? "--in-se-fq $reads" : "--in-fq $reads" + def known_sites_command = known_sites ? known_sites.collect{"--knownSites $it"}.join(' ') : "" + def known_sites_output = known_sites ? "--out-recal-file ${prefix}.table" : "" + def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : '' + """ + ln -sf \$(readlink $fasta) $index/$fasta + + pbrun \\ + fq2bam_meth \\ + --ref $index/$fasta \\ + $in_fq_command \\ + --out-bam ${prefix}.bam \\ + $known_sites_command \\ + $known_sites_output \\ + $num_gpus \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pbrun: \$(echo \$(pbrun version 2>&1) | sed 's/^Please.* //' ) + END_VERSIONS + """ + + stub: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead." + } + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + touch ${prefix}.bam.bai + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pbrun: \$(echo \$(pbrun version 2>&1) | sed 's/^Please.* //' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/parabricks/fq2bammeth/meta.yml b/modules/nf-core/parabricks/fq2bammeth/meta.yml new file mode 100644 index 00000000..4f295b88 --- /dev/null +++ b/modules/nf-core/parabricks/fq2bammeth/meta.yml @@ -0,0 +1,95 @@ +name: "parabricks_fq2bammeth" +description: VIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence +keywords: + - align + - sort + - bqsr + - duplicates + - bwameth +tools: + - "parabricks": + description: "NVIDIA Clara Parabricks GPU-accelerated genomics tools" + homepage: "https://www.nvidia.com/en-us/clara/genomics/" + documentation: "https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html#fq2bam-meth-reference" + licence: ["custom"] + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: fastq.gz files + pattern: "*.fastq.gz" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + - fasta: + type: file + description: reference fasta file - must be unzipped + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing index information + - index: + type: file + description: reference BWA index + pattern: "*.{amb,ann,bwt,pac,sa}" + - - known_sites: + type: file + description: (optional) known sites file(s) for calculating BQSR. markdups must + be true to perform BQSR. + pattern: "*.vcf.gz" +output: + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM file + pattern: "*.bam" + - bai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: index corresponding to sorted BAM file + pattern: "*.bai" + - qc_metrics: + - qc_metrics: + type: directory + description: (optional) optional directory of qc metrics + pattern: "qc_metrics" + - bqsr_table: + - "*.table": + type: file + description: (optional) table from base quality score recalibration calculation, + to be used with parabricks/applybqsr + pattern: "*.table" + - duplicate_metrics: + - duplicate-metrics.txt: + type: file + description: (optional) metrics calculated from marking duplcates in the bam + file + pattern: "*-duplicate-metrics.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@sateeshperi" +maintainers: + - "@sateeshperi" + - "@gallvp" diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test new file mode 100644 index 00000000..ce89e8ca --- /dev/null +++ b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test @@ -0,0 +1,122 @@ +nextflow_process { + + name "Test Process PARABRICKS_FQ2BAMMETH" + script "../main.nf" + process "PARABRICKS_FQ2BAMMETH" + config "./nextflow.config" + + tag "gpu" + tag "bwameth/index" + tag "modules" + tag "parabricks" + tag "parabricks/fq2bammeth" + tag "modules_nfcore" + + setup { + run("BWAMETH_INDEX") { + script "../../../bwameth/index/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + """ + } + } + } + + test("SRR389222 single-end [fastq]") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'test' ], // meta map + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = BWAMETH_INDEX.out.index + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.bai, + process.out.versions + ).match() } + ) + } + } + + test("SRR389222 single-end [fastq] - stub") { + options '-stub' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'test' ], // meta map + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = BWAMETH_INDEX.out.index + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("E.coli paired-end [fastq] - stub") { + options '-stub' + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true), + ] + ]) + input[1] = Channel.of([ + [ id:'test' ], // meta map + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = BWAMETH_INDEX.out.index + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap new file mode 100644 index 00000000..21ae222c --- /dev/null +++ b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap @@ -0,0 +1,166 @@ +{ + "SRR389222 single-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + + ], + "4": [ + + ], + "5": [ + "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf" + ], + "bai": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bqsr_table": [ + + ], + "duplicate_metrics": [ + + ], + "qc_metrics": [ + + ], + "versions": [ + "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-12T11:20:10.809580487" + }, + "E.coli paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + + ], + "4": [ + + ], + "5": [ + "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf" + ], + "bai": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bqsr_table": [ + + ], + "duplicate_metrics": [ + + ], + "qc_metrics": [ + + ], + "versions": [ + "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-12T11:20:18.927598721" + }, + "SRR389222 single-end [fastq]": { + "content": [ + "a7f7ca7b5eb503ab58790d64a0273ed6", + [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam.bai:md5,9ec20dda17ee0441fee0598ec0e2152c" + ] + ], + [ + "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf" + ] + ], + "meta": { + "nf-test": "0.9.1", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-26T21:29:14.709022" + } +} diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/nextflow.config b/modules/nf-core/parabricks/fq2bammeth/tests/nextflow.config new file mode 100644 index 00000000..6ad9d535 --- /dev/null +++ b/modules/nf-core/parabricks/fq2bammeth/tests/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: 'PARABRICKS_FQ2BAMMETH' { + ext.args = '--low-memory' + } + // Ref: https://forums.developer.nvidia.com/t/problem-with-gpu/256825/6 + // Parabricks’s fq2bam requires 24GB of memory. + // Using --low-memory for testing +} \ No newline at end of file diff --git a/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap b/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap index c725d8e8..fdaa4572 100644 --- a/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap +++ b/modules/nf-core/preseq/lcextrap/tests/main.nf.test.snap @@ -13,7 +13,7 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.10.2" }, "timestamp": "2023-11-23T17:20:40.735535" }, @@ -23,7 +23,7 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.10.2" }, "timestamp": "2023-11-23T17:20:51.981746" }, @@ -110,7 +110,7 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.10.2" }, "timestamp": "2023-11-23T17:20:40.72985" }, @@ -128,7 +128,7 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nextflow": "24.10.2" }, "timestamp": "2023-11-23T17:20:51.998533" }, diff --git a/modules/nf-core/qualimap/bamqc/nextflow.config b/modules/nf-core/qualimap/bamqc/nextflow.config deleted file mode 100644 index 004b4047..00000000 --- a/modules/nf-core/qualimap/bamqc/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - withName: QUALIMAP_BAMQC { - ext.args = [ - params.genome.toString().startsWith('GRCh') ? '-gd HUMAN' : '', - params.genome.toString().startsWith('GRCm') ? '-gd MOUSE' : '' - ].join(" ").trim() - } -} \ No newline at end of file diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 4a499727..c23f3a5c 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -18,7 +18,6 @@ process SAMTOOLS_FLAGSTAT { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ samtools \\ diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 493525a9..4443948b 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -19,7 +19,6 @@ process SAMTOOLS_STATS { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--reference ${fasta}" : "" """ diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index 622407ed..b1efd94c 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -1,7 +1,7 @@ channels: - conda-forge - bioconda - dependencies: - bioconda::cutadapt=4.9 - bioconda::trim-galore=0.6.10 + - conda-forge::pigz=2.8 diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 8a2fc54b..e55683ca 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -1,22 +1,22 @@ process TRIMGALORE { - tag "$meta.id" + tag "${meta.id}" label 'process_high' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore%3A0.6.10--hdfd78af_1' : - 'biocontainers/trim-galore:0.6.10--hdfd78af_1' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9b/9becad054093ad4083a961d12733f2a742e11728fe9aa815d678b882b3ede520/data' + : 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d'}" input: tuple val(meta), path(reads) output: tuple val(meta), path("*{3prime,5prime,trimmed,val}*.fq.gz"), emit: reads - tuple val(meta), path("*report.txt") , emit: log , optional: true - tuple val(meta), path("*unpaired*.fq.gz") , emit: unpaired, optional: true - tuple val(meta), path("*.html") , emit: html , optional: true - tuple val(meta), path("*.zip") , emit: zip , optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*report.txt") , emit: log , optional: true + tuple val(meta), path("*unpaired*.fq.gz"), emit: unpaired, optional: true + tuple val(meta), path("*.html") , emit: html , optional: true + tuple val(meta), path("*.zip") , emit: zip , optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -24,14 +24,20 @@ process TRIMGALORE { script: def args = task.ext.args ?: '' // Calculate number of --cores for TrimGalore based on value of task.cpus - // See: https://github.com/FelixKrueger/TrimGalore/blob/master/Changelog.md#version-060-release-on-1-mar-2019 + // See: https://github.com/FelixKrueger/TrimGalore/blob/master/CHANGELOG.md#version-060-release-on-1-mar-2019 // See: https://github.com/nf-core/atacseq/pull/65 def cores = 1 if (task.cpus) { cores = (task.cpus as int) - 4 - if (meta.single_end) cores = (task.cpus as int) - 3 - if (cores < 1) cores = 1 - if (cores > 8) cores = 8 + if (meta.single_end) { + cores = (task.cpus as int) - 3 + } + if (cores < 1) { + cores = 1 + } + if (cores > 8) { + cores = 8 + } } // Added soft-links to original fastqs for consistent naming in MultiQC @@ -40,10 +46,10 @@ process TRIMGALORE { def args_list = args.split("\\s(?=--)").toList() args_list.removeAll { it.toLowerCase().contains('_r2 ') } """ - [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz + [ ! -f ${prefix}.fastq.gz ] && ln -s ${reads} ${prefix}.fastq.gz trim_galore \\ ${args_list.join(' ')} \\ - --cores $cores \\ + --cores ${cores} \\ --gzip \\ ${prefix}.fastq.gz @@ -51,15 +57,17 @@ process TRIMGALORE { "${task.process}": trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') cutadapt: \$(cutadapt --version) + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) END_VERSIONS """ - } else { + } + else { """ [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz trim_galore \\ - $args \\ - --cores $cores \\ + ${args} \\ + --cores ${cores} \\ --paired \\ --gzip \\ ${prefix}_1.fastq.gz \\ @@ -69,6 +77,7 @@ process TRIMGALORE { "${task.process}": trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') cutadapt: \$(cutadapt --version) + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) END_VERSIONS """ } @@ -78,7 +87,8 @@ process TRIMGALORE { if (meta.single_end) { output_command = "echo '' | gzip > ${prefix}_trimmed.fq.gz ;" output_command += "touch ${prefix}.fastq.gz_trimming_report.txt" - } else { + } + else { output_command = "echo '' | gzip > ${prefix}_1_trimmed.fq.gz ;" output_command += "touch ${prefix}_1.fastq.gz_trimming_report.txt ;" output_command += "echo '' | gzip > ${prefix}_2_trimmed.fq.gz ;" @@ -91,6 +101,7 @@ process TRIMGALORE { "${task.process}": trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//') cutadapt: \$(cutadapt --version) + pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' ) END_VERSIONS """ } diff --git a/modules/nf-core/trimgalore/tests/main.nf.test b/modules/nf-core/trimgalore/tests/main.nf.test index 2a3dbbb0..37b054fc 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test +++ b/modules/nf-core/trimgalore/tests/main.nf.test @@ -39,7 +39,7 @@ nextflow_process { { assert path(process.out.log.get(0).get(1)).getText().contains(report1_line) } } }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(path(process.out.versions.get(0)).yaml).match() }, ) } } @@ -61,7 +61,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + process.out, + path(process.out.versions.get(0)).yaml + ).match() }, ) } } @@ -118,7 +121,7 @@ nextflow_process { { assert path(process.out.log.get(0).get(1).get(1)).getText().contains(report2_line) } } }, - { assert snapshot(process.out.versions).match() } + { assert snapshot(path(process.out.versions.get(0)).yaml).match() }, ) } } @@ -143,8 +146,9 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot(process.out).match() }, + { assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") }, ) } } -} +} \ No newline at end of file diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 21da8493..4c731806 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -1,15 +1,19 @@ { "test_trimgalore_single_end": { "content": [ - [ - "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" - ] + { + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.9, + "pigz": 2.8 + } + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-22T19:23:17.969056957" + "timestamp": "2024-12-05T22:56:18.454197" }, "test_trimgalore_single_end - stub": { "content": [ @@ -42,7 +46,7 @@ ], "5": [ - "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" + "versions.yml:md5,5928323d579768de37e83c56c821757f" ], "html": [ @@ -69,18 +73,25 @@ ], "versions": [ - "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" + "versions.yml:md5,5928323d579768de37e83c56c821757f" ], "zip": [ ] + }, + { + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.9, + "pigz": 2.8 + } } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-22T19:23:28.617831159" + "timestamp": "2024-12-05T22:56:22.085472" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -119,7 +130,7 @@ ], "5": [ - "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" + "versions.yml:md5,5928323d579768de37e83c56c821757f" ], "html": [ @@ -152,7 +163,7 @@ ], "versions": [ - "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" + "versions.yml:md5,5928323d579768de37e83c56c821757f" ], "zip": [ @@ -160,21 +171,41 @@ } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-05T22:44:33.751013" + }, + "versions": { + "content": [ + { + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.9, + "pigz": 2.8 + } + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-22T19:23:51.539787731" + "timestamp": "2024-12-05T22:57:28.77107" }, "test_trimgalore_paired_end": { "content": [ - [ - "versions.yml:md5,81a0b49f3a9e1315fe564f9946eb8c50" - ] + { + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.9, + "pigz": 2.8 + } + } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-22T19:23:41.16485915" + "timestamp": "2024-12-05T22:56:27.019872" } } \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index 4821c55b..275b2202 100644 --- a/nextflow.config +++ b/nextflow.config @@ -10,82 +10,87 @@ params { // Input options - input = null + input = null // References - genome = null - igenomes_base = 's3://ngi-igenomes/igenomes/' - igenomes_ignore = false + genome = null + igenomes_base = 's3://ngi-igenomes/igenomes/' + igenomes_ignore = false // MultiQC options - multiqc_config = null - multiqc_title = null - multiqc_logo = null - max_multiqc_email_size = '25.MB' - multiqc_methods_description = null + multiqc_config = null + multiqc_title = null + multiqc_logo = null + max_multiqc_email_size = '25.MB' + multiqc_methods_description = null // Intermediate files - save_reference = false - save_align_intermeds = false - unmapped = false - save_trimmed = false + save_reference = false + save_align_intermeds = false + unmapped = false + save_trimmed = false // Alignment options - aligner = 'bismark' - comprehensive = false - - // Qualimap options - bamqc_regions_file = null + aligner = 'bismark' + comprehensive = false // Library presets - pbat = false - rrbs = false - slamseq = false - em_seq = false - single_cell = false - accel = false - cegx = false - epignome = false - zymo = false + pbat = false + rrbs = false + slamseq = false + em_seq = false + single_cell = false + accel = false + cegx = false + epignome = false + zymo = false // Trimming options - clip_r1 = 0 - clip_r2 = 0 - three_prime_clip_r1 = 0 - three_prime_clip_r2 = 0 - nextseq_trim = 0 - length_trim = null + clip_r1 = 0 + clip_r2 = 0 + three_prime_clip_r1 = 0 + three_prime_clip_r2 = 0 + nextseq_trim = 0 + length_trim = null // Bismark options - non_directional = false - cytosine_report = false - relax_mismatches = false - num_mismatches = 0.6 + non_directional = false + cytosine_report = false + relax_mismatches = false + num_mismatches = 0.6 // 0.6 will allow a penalty of bp * -0.6 // For 100bp reads, this is -60. Mismatches cost -6, gap opening -5 and gap extension -2 // So -60 would allow 10 mismatches or ~ 8 x 1-2bp indels // Bismark default is 0.2 (L,0,-0.2), Bowtie2 default is 0.6 (L,0,-0.6) - meth_cutoff = null - no_overlap = true - ignore_r1 = 0 - ignore_r2 = 2 - ignore_3prime_r1 = 0 - ignore_3prime_r2 = 2 - known_splices = null - local_alignment = false - minins = null - maxins = null - nomeseq = false + meth_cutoff = null + no_overlap = true + ignore_r1 = 0 + ignore_r2 = 2 + ignore_3prime_r1 = 0 + ignore_3prime_r2 = 2 + known_splices = null + local_alignment = false + minins = null + maxins = null + nomeseq = false // bwa-meth options - min_depth = 0 - ignore_flags = false - methyl_kit = false + use_gpu = false + min_depth = 0 + ignore_flags = false + methyl_kit = false // Skipping options - skip_trimming = false - skip_deduplication = false - skip_multiqc = false + skip_trimming = false + skip_deduplication = false + skip_multiqc = false + + // Run options + run_preseq = false + run_qualimap = false + + // Qualimap options + bamqc_regions_file = null // Boilerplate options outdir = null @@ -99,11 +104,10 @@ params { help_full = false show_hidden = false version = false - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/methylseq' - - // Config options - config_profile_name = null - config_profile_description = null + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/' + trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options + config_profile_name = null + config_profile_description = null custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" @@ -216,10 +220,13 @@ profiles { executor.cpus = 4 executor.memory = 8.GB } + gpu { + docker.runOptions = '-u $(id -u):$(id -g) --gpus all' + apptainer.runOptions = '--nv' + singularity.runOptions = '--nv' + } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } - test_ci { params.pipelines_testdata_base_path = './test-datasets/' } - dev { nextflow.enable.configProcessNamesValidation = true } } // Load nf-core custom profiles from different Institutions @@ -264,32 +271,97 @@ set -C # No clobber - prevent output redirection from overwriting files. // Disable process selector warnings by default. Use debug profile to enable warnings. nextflow.enable.configProcessNamesValidation = false -def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true - file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html" } report { enabled = true - file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html" } trace { enabled = true - file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt" + file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt" } dag { enabled = true - file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html" + file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html" } manifest { name = 'nf-core/methylseq' - author = """Phil Ewels, Sateesh Peri""" + contributors = [ + [ + name: 'Phil Ewels', + affiliation: 'Seqera', + email: 'phil.ewels@seqera.io', + github: 'https://github.com/ewels', + contribution: ['author', 'contributor'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0003-4101-2502' + ], + [ + name: 'Sateesh Peri', + affiliation: 'PeriMatrixIT', + email: 'perisateesh@gmail.com', + github: 'https://github.com/sateeshperi', + contribution: ['author', 'maintainer'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0002-9879-9070' + ], + [ + name: 'Felix Krueger', + affiliation: 'Altos Lab', + email: 'fkrueger@altoslabs.com', + github: 'https://github.com/FelixKrueger', + contribution: ['maintainer', 'contributor'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0002-5513-3324' + ], + [ + name: 'Edmund Miller', + affiliation: 'Department of Biological Sciences and Center for Systems Biology, University of Texas at Dallas, Texas, USA', + email: 'nf-core@edmundmiller.dev', + github: 'https://github.com/edmundmiller', + contribution: ['maintainer', 'contributor'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0002-2398-0334' + ], + [ + name: 'Rickard Hammarén', + affiliation: '', + email: '', + github: 'https://github.com/Hammarn', + contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + [ + name: 'Alexander Peltzer', + affiliation: 'Boehringer Ingelheim Pharma GmBh & Co KG', + email: 'alex.peltzer@gmail.com', + github: 'https://github.com/apeltzer', + contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0002-6503-2180' + ], + [ + name: 'Patrick Hüther', + affiliation: '', + email: '', + github: 'https://github.com/phue', + contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '' + ], + [ + name: 'Maxime U Garcia', + affiliation: 'Seqera', + email: 'maxime.garcia@seqera.io', + github: 'https://github.com/maxulysse', + contribution: ['contributor'], // List of contribution types ('author', 'maintainer' or 'contributor') + orcid: '0000-0003-2827-9261' + ], + ] homePage = 'https://github.com/nf-core/methylseq' description = """Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.""" mainScript = 'main.nf' - nextflowVersion = '!>=24.04.2' - version = '2.7.1' + defaultBranch = 'master' + nextflowVersion = '!>=24.10.2' + version = '3.0.0' doi = '10.5281/zenodo.1343417' } @@ -300,9 +372,10 @@ plugins { validation { defaultIgnoreParams = ["genomes"] + monochromeLogs = params.monochrome_logs help { enabled = true - command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + command = "nextflow run nf-core/methylseq -profile --input samplesheet.csv --outdir " fullParameter = "help_full" showHiddenParameter = "show_hidden" beforeText = """ @@ -312,15 +385,15 @@ validation { \033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m \033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m \033[0;32m`._,._,\'\033[0m -\033[0;35m ${manifest.name} ${manifest.version}\033[0m +\033[0;35m nf-core/methylseq ${manifest.version}\033[0m -\033[2m----------------------------------------------------\033[0m- """ - afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} + afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/${manifest.name}/blob/master/CITATIONS.md + https://github.com/nf-core/methylseq/blob/master/CITATIONS.md """ } summary { diff --git a/nextflow_schema.json b/nextflow_schema.json index ca54aada..57849217 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -374,12 +374,18 @@ } } }, - "bwa_meth_options": { + "bwameth_options": { "title": "bwa-meth options", "type": "object", "description": "", "default": "", "properties": { + "use_gpu": { + "type": "boolean", + "description": "Run Parabricks GPU-accelerated fq2bammeth module for alignment", + "default": false, + "fa_icon": "fas fa-dot-circle" + }, "min_depth": { "type": "integer", "description": "Specify a minimum read coverage for MethylDackel to report a methylation call.", @@ -442,6 +448,25 @@ }, "fa_icon": "fas fa-fast-forward" }, + "run_pipeline_steps": { + "title": "Run pipeline steps", + "type": "object", + "description": "", + "default": "", + "properties": { + "run_preseq": { + "type": "boolean", + "description": "Run preseq/lcextrap tool", + "fa_icon": "fas fa-fast-forward" + }, + "run_qualimap": { + "type": "boolean", + "description": "Run qualimap/bamqc tool", + "fa_icon": "fas fa-fast-forward" + } + }, + "fa_icon": "fas fa-fast-forward" + }, "institutional_config_options": { "title": "Institutional config options", "type": "object", @@ -576,7 +601,13 @@ "type": "string", "fa_icon": "far fa-check-circle", "description": "Base URL or local path to location of pipeline test dataset files", - "default": "https://raw.githubusercontent.com/nf-core/test-datasets/methylseq", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/", + "hidden": true + }, + "trace_report_suffix": { + "type": "string", + "fa_icon": "far calendar", + "description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.", "hidden": true } } @@ -605,7 +636,7 @@ "$ref": "#/$defs/bismark_options" }, { - "$ref": "#/$defs/bwa_meth_options" + "$ref": "#/$defs/bwameth_options" }, { "$ref": "#/$defs/qualimap_options" @@ -613,6 +644,9 @@ { "$ref": "#/$defs/skip_pipeline_steps" }, + { + "$ref": "#/$defs/run_pipeline_steps" + }, { "$ref": "#/$defs/generic_options" }, diff --git a/nf-test.config b/nf-test.config index b7a7023a..e0bb0c55 100644 --- a/nf-test.config +++ b/nf-test.config @@ -12,11 +12,11 @@ config { profile "test" // List of filenames or patterns that should be trigger a full test run - triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'conf/test_full.config' + triggers 'nextflow.config', 'nf-test.config' // load the necessary plugins plugins { - load "nft-bam@0.3.0" + load "nft-bam@0.5.0" load "nft-utils@0.0.3" } } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json new file mode 100644 index 00000000..788e0b89 --- /dev/null +++ b/ro-crate-metadata.json @@ -0,0 +1,253 @@ +{ + "@context": "https://w3id.org/ro/crate/1.1/context", + "@graph": [ + { + "@id": "./", + "@type": "Dataset", + "creativeWorkStatus": "Stable", + "datePublished": "2024-12-16T12:03:17+00:00", + "description": "

\n \n \n \"nf-core/methylseq\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/methylseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/methylseq/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/methylseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/methylseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/methylseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1343417-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1343417)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.10.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/methylseq)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23methylseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/methylseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/methylseq** is a bioinformatics analysis pipeline used for Methylation (Bisulfite) sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results.\n\n![nf-core/methylseq metro map](docs/images/3.0.0_metromap.png)\n\nThe pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker / Singularity containers making installation trivial and results highly reproducible.\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/methylseq/results).\n\n> Read more about **Bisulfite Sequencing & Three-Base Aligners** used in this pipeline [here](./docs/bs-seq-primer.md)\n\n## Pipeline Summary\n\nThe pipeline allows you to choose between running either [Bismark](https://github.com/FelixKrueger/Bismark) or [bwa-meth](https://github.com/brentp/bwa-meth) / [MethylDackel](https://github.com/dpryan79/methyldackel).\n\nChoose between workflows by using `--aligner bismark` (default, uses bowtie2 for alignment), `--aligner bismark_hisat` or `--aligner bwameth`. For higher performance, the pipeline can leverage the [Parabricks implementation of bwa-meth (fq2bammeth)](https://docs.nvidia.com/clara/parabricks/latest/documentation/tooldocs/man_fq2bam_meth.html), which implements the baseline tool `bwa-meth` in a performant method using fq2bam (BWA-MEM + GATK) as a backend for processing on GPU. To use this option, include the `--use_gpu` flag along with `--aligner bwameth`.\n\n| Step | Bismark workflow | bwa-meth workflow |\n| -------------------------------------------- | ------------------------ | --------------------- |\n| Generate Reference Genome Index _(optional)_ | Bismark | bwa-meth |\n| Merge re-sequenced FastQ files | cat | cat |\n| Raw data QC | FastQC | FastQC |\n| Adapter sequence trimming | Trim Galore! | Trim Galore! |\n| Align Reads | Bismark (bowtie2/hisat2) | bwa-meth |\n| Deduplicate Alignments | Bismark | Picard MarkDuplicates |\n| Extract methylation calls | Bismark | MethylDackel |\n| Sample report | Bismark | - |\n| Summary Report | Bismark | - |\n| Alignment QC | Qualimap _(optional)_ | Qualimap _(optional)_ |\n| Sample complexity | Preseq _(optional)_ | Preseq _(optional)_ |\n| Project Report | MultiQC | MultiQC |\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,fastq_1,fastq_2,genome\nSRR389222_sub1,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz,,\nSRR389222_sub2,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz,,\nSRR389222_sub3,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz,,\nEcoli_10K_methylated,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz,https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz,\n```\n\n> Each row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nNow, you can run the pipeline using default parameters as:\n\n```bash\nnextflow run nf-core/methylseq --input samplesheet.csv --outdir --genome GRCh37 -profile \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/methylseq/usage) and the [parameter documentation](https://nf-co.re/methylseq/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/methylseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/methylseq/output).\n\n## Credits\n\nnf-core/methylseq was originally written by Phil Ewels ([@ewels](https://github.com/ewels)), and Sateesh Peri ([@sateeshperi](https://github.com/sateeshperi)) is its active maintainer.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- Felix Krueger ([@FelixKrueger](https://github.com/FelixKrueger))\n- Edmund Miller ([@EMiller88](https://github.com/emiller88))\n- Rickard Hammar\u00e9n ([@Hammarn](https://github.com/Hammarn/))\n- Alexander Peltzer ([@apeltzer](https://github.com/apeltzer/))\n- Patrick H\u00fcther ([@phue](https://github.com/phue/))\n- Maxime U Garcia ([@maxulysse](https://github.com/maxulysse/))\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#methylseq` channel](https://nfcore.slack.com/channels/methylseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/methylseq for your analysis, please cite it using the following doi: [10.5281/zenodo.1343417](https://doi.org/10.5281/zenodo.1343417)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "hasPart": [ + { + "@id": "main.nf" + }, + { + "@id": "assets/" + }, + { + "@id": "conf/" + }, + { + "@id": "docs/" + }, + { + "@id": "docs/images/" + }, + { + "@id": "modules/" + }, + { + "@id": "modules/nf-core/" + }, + { + "@id": "workflows/" + }, + { + "@id": "subworkflows/" + }, + { + "@id": "nextflow.config" + }, + { + "@id": "README.md" + }, + { + "@id": "nextflow_schema.json" + }, + { + "@id": "CHANGELOG.md" + }, + { + "@id": "LICENSE" + }, + { + "@id": "CODE_OF_CONDUCT.md" + }, + { + "@id": "CITATIONS.md" + }, + { + "@id": "modules.json" + }, + { + "@id": "docs/usage.md" + }, + { + "@id": "docs/output.md" + }, + { + "@id": ".nf-core.yml" + }, + { + "@id": ".pre-commit-config.yaml" + }, + { + "@id": ".prettierignore" + } + ], + "isBasedOn": "https://github.com/nf-core/methylseq", + "license": "MIT", + "mainEntity": { + "@id": "main.nf" + }, + "name": "nf-core/methylseq" + }, + { + "@id": "ro-crate-metadata.json", + "@type": "CreativeWork", + "about": { + "@id": "./" + }, + "conformsTo": [ + { + "@id": "https://w3id.org/ro/crate/1.1" + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0" + } + ] + }, + { + "@id": "main.nf", + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "dateCreated": "", + "dateModified": "2024-12-16T12:03:17Z", + "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", + "keywords": [ + "nf-core", + "nextflow", + "bisulfite-sequencing", + "dna-methylation", + "em-seq", + "epigenome", + "epigenomics", + "methyl-seq", + "pbat", + "rrbs" + ], + "license": ["MIT"], + "name": ["nf-core/methylseq"], + "programmingLanguage": { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" + }, + "sdPublisher": { + "@id": "https://nf-co.re/" + }, + "url": ["https://github.com/nf-core/methylseq", "https://nf-co.re/methylseq/3.0.0/"], + "version": ["3.0.0"] + }, + { + "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", + "@type": "ComputerLanguage", + "identifier": { + "@id": "https://www.nextflow.io/" + }, + "name": "Nextflow", + "url": { + "@id": "https://www.nextflow.io/" + }, + "version": "!>=24.10.2" + }, + { + "@id": "assets/", + "@type": "Dataset", + "description": "Additional files" + }, + { + "@id": "conf/", + "@type": "Dataset", + "description": "Configuration files" + }, + { + "@id": "docs/", + "@type": "Dataset", + "description": "Markdown files for documenting the pipeline" + }, + { + "@id": "docs/images/", + "@type": "Dataset", + "description": "Images for the documentation files" + }, + { + "@id": "modules/", + "@type": "Dataset", + "description": "Modules used by the pipeline" + }, + { + "@id": "modules/nf-core/", + "@type": "Dataset", + "description": "nf-core modules" + }, + { + "@id": "workflows/", + "@type": "Dataset", + "description": "Main pipeline workflows to be executed in main.nf" + }, + { + "@id": "subworkflows/", + "@type": "Dataset", + "description": "Smaller subworkflows" + }, + { + "@id": "nextflow.config", + "@type": "File", + "description": "Main Nextflow configuration file" + }, + { + "@id": "README.md", + "@type": "File", + "description": "Basic pipeline usage information" + }, + { + "@id": "nextflow_schema.json", + "@type": "File", + "description": "JSON schema for pipeline parameter specification" + }, + { + "@id": "CHANGELOG.md", + "@type": "File", + "description": "Information on changes made to the pipeline" + }, + { + "@id": "LICENSE", + "@type": "File", + "description": "The license - should be MIT" + }, + { + "@id": "CODE_OF_CONDUCT.md", + "@type": "File", + "description": "The nf-core code of conduct" + }, + { + "@id": "CITATIONS.md", + "@type": "File", + "description": "Citations needed when using the pipeline" + }, + { + "@id": "modules.json", + "@type": "File", + "description": "Version information for modules from nf-core/modules" + }, + { + "@id": "docs/usage.md", + "@type": "File", + "description": "Usage documentation" + }, + { + "@id": "docs/output.md", + "@type": "File", + "description": "Output documentation" + }, + { + "@id": ".nf-core.yml", + "@type": "File", + "description": "nf-core configuration file, configuring template features and linting rules" + }, + { + "@id": ".pre-commit-config.yaml", + "@type": "File", + "description": "Configuration file for pre-commit hooks" + }, + { + "@id": ".prettierignore", + "@type": "File", + "description": "Ignore file for prettier" + }, + { + "@id": "https://nf-co.re/", + "@type": "Organization", + "name": "nf-core", + "url": "https://nf-co.re/" + } + ] +} diff --git a/subworkflows/local/bismark/main.nf b/subworkflows/local/bismark/main.nf deleted file mode 100644 index e94c0692..00000000 --- a/subworkflows/local/bismark/main.nf +++ /dev/null @@ -1,159 +0,0 @@ -/* - * Bismark subworkflow - */ -include { BISMARK_ALIGN } from '../../../modules/nf-core/bismark/align/main' -include { SAMTOOLS_SORT as SAMTOOLS_SORT_ALIGNED } from '../../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_SORT as SAMTOOLS_SORT_DEDUPLICATED } from '../../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_DEDUPLICATED } from '../../../modules/nf-core/samtools/index/main' -include { BISMARK_DEDUPLICATE } from '../../../modules/nf-core/bismark/deduplicate/main' -include { BISMARK_METHYLATIONEXTRACTOR } from '../../../modules/nf-core/bismark/methylationextractor/main' -include { BISMARK_COVERAGE2CYTOSINE } from '../../../modules/nf-core/bismark/coverage2cytosine/main' -include { BISMARK_REPORT } from '../../../modules/nf-core/bismark/report/main' -include { BISMARK_SUMMARY } from '../../../modules/nf-core/bismark/summary/main' - -workflow BISMARK { - take: - reads // channel: [ val(meta), [ reads ] ] - fasta // channel: /path/to/genome.fasta - bismark_index // channel: /path/to/BismarkIndex/ - skip_deduplication // boolean: whether to deduplicate alignments - cytosine_report // boolean: whether the run coverage2cytosine - - main: - - ch_versions = Channel.empty() - /* - * Align with bismark - */ - BISMARK_ALIGN ( - reads, - fasta, - bismark_index - ) - BISMARK_ALIGN.out.bam.dump(tag: 'BISMARK_ALIGN: bam') - BISMARK_ALIGN.out.report.dump(tag: 'BISMARK_ALIGN: report') - - ch_versions = ch_versions.mix(BISMARK_ALIGN.out.versions) - - /* - * Sort raw output BAM - */ - SAMTOOLS_SORT_ALIGNED( - BISMARK_ALIGN.out.bam, - [[:],[]] // Empty map and list as is optional input but required for nextflow - ) - SAMTOOLS_SORT_ALIGNED.out.bam.dump(tag: 'BISMARK/SAMTOOLS_SORT_ALIGNED: bam') - - ch_versions = ch_versions.mix(SAMTOOLS_SORT_ALIGNED.out.versions) - - if (skip_deduplication) { - alignments = BISMARK_ALIGN.out.bam - alignment_reports = BISMARK_ALIGN.out.report.map{ meta, report -> [ meta, report, [] ] } - - alignments.dump(tag: 'BISMARK/skip_deduplication: alignments') - alignment_reports.dump(tag: 'BISMARK/skip_deduplication: alignment_reports') - } else { - /* - * Run deduplicate_bismark - */ - BISMARK_DEDUPLICATE(BISMARK_ALIGN.out.bam) - - alignments = BISMARK_DEDUPLICATE.out.bam - alignment_reports = BISMARK_ALIGN.out.report.join(BISMARK_DEDUPLICATE.out.report) - ch_versions = ch_versions.mix(BISMARK_DEDUPLICATE.out.versions) - - alignments.dump(tag: 'BISMARK_DEDUPLICATE: alignments') - alignment_reports.dump(tag: 'BISMARK_DEDUPLICATE: alignment_reports') - } - - /* - * Run bismark_methylation_extractor - */ - BISMARK_METHYLATIONEXTRACTOR ( - alignments, - bismark_index - ) - BISMARK_METHYLATIONEXTRACTOR.out.report.dump(tag: 'BISMARK_METHYLATIONEXTRACTOR: report') - BISMARK_METHYLATIONEXTRACTOR.out.mbias.dump(tag: 'BISMARK_METHYLATIONEXTRACTOR: mbias') - - ch_versions = ch_versions.mix(BISMARK_METHYLATIONEXTRACTOR.out.versions) - - /* - * Run coverage2cytosine - */ - if (cytosine_report) { - BISMARK_COVERAGE2CYTOSINE ( - BISMARK_METHYLATIONEXTRACTOR.out.coverage, - fasta, - bismark_index - ) - BISMARK_COVERAGE2CYTOSINE.out.report.dump(tag: 'BISMARK_COVERAGE2CYTOSINE: report') - BISMARK_COVERAGE2CYTOSINE.out.coverage.dump(tag: 'BISMARK_COVERAGE2CYTOSINE: coverage') - BISMARK_COVERAGE2CYTOSINE.out.summary.dump(tag: 'BISMARK_COVERAGE2CYTOSINE: summary') - - ch_versions = ch_versions.mix(BISMARK_COVERAGE2CYTOSINE.out.versions) - } - - /* - * Generate bismark sample reports - */ - BISMARK_REPORT ( - alignment_reports - .join(BISMARK_METHYLATIONEXTRACTOR.out.report) - .join(BISMARK_METHYLATIONEXTRACTOR.out.mbias) - ) - BISMARK_REPORT.out.report.dump(tag: 'BISMARK_REPORT: report') - - ch_versions = ch_versions.mix(BISMARK_REPORT.out.versions) - - /* - * Generate bismark summary report - */ - BISMARK_SUMMARY ( - BISMARK_ALIGN.out.bam.collect{ it[1].name }.ifEmpty([]), - alignment_reports.collect{ it[1] }.ifEmpty([]), - alignment_reports.collect{ it[2] }.ifEmpty([]), - BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ it[1] }.ifEmpty([]), - BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ it[1] }.ifEmpty([]) - ) - BISMARK_SUMMARY.out.summary.dump(tag: 'BISMARK_REPORT: summary') - - ch_versions = ch_versions.mix(BISMARK_SUMMARY.out.versions) - - /* - * MODULE: Run samtools sort - */ - SAMTOOLS_SORT_DEDUPLICATED ( - alignments, - [[:],[]] // Empty map and list as is optional input but required for nextflow - ) - SAMTOOLS_SORT_DEDUPLICATED.out.bam.dump(tag: 'BISMARK/SAMTOOLS_SORT_DEDUPLICATED: bam') - - ch_versions = ch_versions.mix(SAMTOOLS_SORT_DEDUPLICATED.out.versions) - - /* - * MODULE: Run samtools index on dedup bam - */ - SAMTOOLS_INDEX_DEDUPLICATED(SAMTOOLS_SORT_DEDUPLICATED.out.bam) - - SAMTOOLS_INDEX_DEDUPLICATED.out.bai.dump(tag: 'BISMARK/SAMTOOLS_INDEX_DEDUPLICATED: bai') - - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_DEDUPLICATED.out.versions) - - /* - * Collect MultiQC inputs - */ - BISMARK_SUMMARY.out.summary.ifEmpty([]) - .mix(alignment_reports.collect{ it[1] }) - .mix(alignment_reports.collect{ it[2] }) - .mix(BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ it[1] }) - .mix(BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ it[1] }) - .mix(BISMARK_REPORT.out.report.collect{ it[1] }) - .set{ multiqc_files } - - emit: - bam = SAMTOOLS_SORT_ALIGNED.out.bam // channel: [ val(meta), [ bam ] ] ## sorted, non-deduplicated (raw) BAM from aligner - dedup = SAMTOOLS_SORT_DEDUPLICATED.out.bam // channel: [ val(meta), [ bam ] ] ## sorted, possibly deduplicated BAM - mqc = multiqc_files // path: *{html,txt} - versions = ch_versions // path: *.version.txt -} diff --git a/subworkflows/local/bismark/nextflow.config b/subworkflows/local/bismark/nextflow.config deleted file mode 100644 index d58d65ad..00000000 --- a/subworkflows/local/bismark/nextflow.config +++ /dev/null @@ -1,32 +0,0 @@ - -includeConfig "../../../modules/nf-core/bismark/align/nextflow.config" -includeConfig "../../../modules/nf-core/samtools/sort/nextflow.config" -includeConfig "../../../modules/nf-core/bismark/deduplicate/nextflow.config" -includeConfig "../../../modules/nf-core/bismark/methylationextractor/nextflow.config" -includeConfig "../../../modules/nf-core/bismark/coverage2cytosine/nextflow.config" -includeConfig "../../../modules/nf-core/bismark/report/nextflow.config" -includeConfig "../../../modules/nf-core/bismark/summary/nextflow.config" - -process { - withName: SAMTOOLS_SORT_DEDUPLICATED { - ext.prefix = { "${meta.id}.deduplicated.sorted" } - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/deduplicated/" }, - mode: params.publish_dir_mode, - pattern: "*.deduplicated.sorted.bam" - ] - ] - } - - withName: SAMTOOLS_INDEX_DEDUPLICATED { - ext.args = "" - publishDir = [ - [ - path: { "${params.outdir}/${params.aligner}/deduplicated/" }, - mode: params.publish_dir_mode, - pattern: "*.bai" - ] - ] - } -} diff --git a/subworkflows/local/bismark/tests/bismark_hisat.nf.test b/subworkflows/local/bismark/tests/bismark_hisat.nf.test deleted file mode 100644 index 1f1070b3..00000000 --- a/subworkflows/local/bismark/tests/bismark_hisat.nf.test +++ /dev/null @@ -1,70 +0,0 @@ -nextflow_workflow { - - name "Test Workflow BISMARK_HISAT" - script "../main.nf" - workflow "BISMARK" - config "../nextflow.config" - - setup { - run("UNTAR") { - script "../../../../modules/nf-core/untar/main.nf" - process { - """ - input[0] = [ - [:], - file(params.pipelines_testdata_base_path + 'reference/Hisat2_Index.tar.gz', checkIfExists: true) - ] - """ - } - } - } - - test("Bismark_Hisat | save_reference") { - - when { - params { - aligner = "bismark_hisat" - publish_dir_mode = 'copy' - unmapped = false - save_align_intermeds = false - skip_deduplication = false - cytosine_report = false - rrbs = false - nomeseq = false - slamseq = false - save_reference = true - outdir = "results" - } - workflow { - """ - - input[0] = Channel.of([ - [ id:'test', single_end:true ], - file(params.pipelines_testdata_base_path + 'testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) - ]) - input[1] = Channel.of([ - [:], - file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) - ]) - input[2] = UNTAR.out.untar - input[3] = params.skip_deduplication - input[4] = params.cytosine_report - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.bam.collect { bam(it[1]).getReadsMD5() }, - workflow.out.dedup.collect { bam(it[1]).getReadsMD5() }, - //workflow.out.mqc, - workflow.out.versions - ).match() } - ) - } - - } - -} diff --git a/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap b/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap deleted file mode 100644 index a531a2e7..00000000 --- a/subworkflows/local/bismark/tests/bismark_hisat.nf.test.snap +++ /dev/null @@ -1,27 +0,0 @@ -{ - "Bismark_Hisat | save_reference": { - "content": [ - [ - "3a6485d719fcaf868c7f95c8f10a3f3c" - ], - [ - "dae445da532c973dc9149f3ceba2d2c5" - ], - [ - "versions.yml:md5,2273d537ccb64f2260adeb6844523d73", - "versions.yml:md5,6a04613f312dd68246d992a7f6fa03a5", - "versions.yml:md5,c06f3e25000330e948f7a35708270f3f", - "versions.yml:md5,c2ad6c469b4d15c963f03b2228376a80", - "versions.yml:md5,cb4a7015750ef1e0e504c56acb72a799", - "versions.yml:md5,cb8dda62996be2045f2ad33831c6b74c", - "versions.yml:md5,cd3f634936e8c40265e766e5f5d07f15", - "versions.yml:md5,cfb4c81c53e84715cbf50b702a84e457" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-20T11:17:46.351442694" - } -} diff --git a/subworkflows/local/bismark/tests/main.nf.test b/subworkflows/local/bismark/tests/main.nf.test deleted file mode 100644 index b38cbdbc..00000000 --- a/subworkflows/local/bismark/tests/main.nf.test +++ /dev/null @@ -1,70 +0,0 @@ -nextflow_workflow { - - name "Test Workflow BISMARK" - script "../main.nf" - workflow "BISMARK" - config "../nextflow.config" - - setup { - run("UNTAR") { - script "../../../../modules/nf-core/untar/main.nf" - process { - """ - input[0] = [ - [:], - file(params.pipelines_testdata_base_path + 'reference/Bowtie2_Index.tar.gz', checkIfExists: true) - ] - """ - } - } - } - - test("Bismark | save_reference") { - - when { - params { - aligner = "bismark" - publish_dir_mode = 'copy' - unmapped = false - save_align_intermeds = false - skip_deduplication = false - cytosine_report = false - rrbs = false - nomeseq = false - slamseq = false - save_reference = true - outdir = "results" - } - workflow { - """ - - input[0] = Channel.of([ - [ id:'test', single_end:true ], - file(params.pipelines_testdata_base_path + 'testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) - ]) - input[1] = Channel.of([ - [:], - file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) - ]) - input[2] = UNTAR.out.untar - input[3] = params.skip_deduplication - input[4] = params.cytosine_report - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.bam.collect { bam(it[1]).getReadsMD5() }, - workflow.out.dedup.collect { bam(it[1]).getReadsMD5() }, - //workflow.out.mqc, - workflow.out.versions - ).match() } - ) - } - - } - -} diff --git a/subworkflows/local/bismark/tests/main.nf.test.snap b/subworkflows/local/bismark/tests/main.nf.test.snap deleted file mode 100644 index 6757ea79..00000000 --- a/subworkflows/local/bismark/tests/main.nf.test.snap +++ /dev/null @@ -1,27 +0,0 @@ -{ - "Bismark | save_reference": { - "content": [ - [ - "d6951f6d3381e22becf62553a37c0f3f" - ], - [ - "35d55bee1ca653931716e40dac4aba30" - ], - [ - "versions.yml:md5,2273d537ccb64f2260adeb6844523d73", - "versions.yml:md5,6a04613f312dd68246d992a7f6fa03a5", - "versions.yml:md5,c06f3e25000330e948f7a35708270f3f", - "versions.yml:md5,c2ad6c469b4d15c963f03b2228376a80", - "versions.yml:md5,cb4a7015750ef1e0e504c56acb72a799", - "versions.yml:md5,cb8dda62996be2045f2ad33831c6b74c", - "versions.yml:md5,cd3f634936e8c40265e766e5f5d07f15", - "versions.yml:md5,cfb4c81c53e84715cbf50b702a84e457" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-20T11:14:29.732866935" - } -} diff --git a/subworkflows/local/bwameth/main.nf b/subworkflows/local/bwameth/main.nf deleted file mode 100644 index 04608995..00000000 --- a/subworkflows/local/bwameth/main.nf +++ /dev/null @@ -1,136 +0,0 @@ -/* - * bwameth subworkflow - */ -include { BWAMETH_ALIGN } from '../../../modules/nf-core/bwameth/align/main' -include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_ALIGNMENTS } from '../../../modules/nf-core/samtools/index/main' -include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' -include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' -include { PICARD_MARKDUPLICATES } from '../../../modules/nf-core/picard/markduplicates/main' -include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_DEDUPLICATED } from '../../../modules/nf-core/samtools/index/main' -include { METHYLDACKEL_EXTRACT } from '../../../modules/nf-core/methyldackel/extract/main' -include { METHYLDACKEL_MBIAS } from '../../../modules/nf-core/methyldackel/mbias/main' - -workflow BWAMETH { - take: - reads // channel: [ val(meta), [ reads ] ] - bwameth_index // channel: /path/to/bwa_index/ - fasta // channel: /path/to/genome.fa - fasta_index // channel: /path/to/genome.fa.fai - skip_deduplication // boolean: whether to deduplicate alignments - - main: - ch_versions = Channel.empty() - - /* - * Align with bwameth - */ - BWAMETH_ALIGN ( - reads, - fasta, - bwameth_index - ) - BWAMETH_ALIGN.out.bam.dump(tag: 'BWAMETH_ALIGN: bam') - - ch_versions = ch_versions.mix(BWAMETH_ALIGN.out.versions) - - /* - * Sort raw output BAM - */ - SAMTOOLS_SORT ( - BWAMETH_ALIGN.out.bam, - [[:],[]] // Empty map and list as is optional input but required for nextflow - ) - SAMTOOLS_SORT.out.bam.dump(tag: 'BWAMETH/SAMTOOLS_SORT: bam') - - ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) - - /* - * Run samtools index on alignment - */ - SAMTOOLS_INDEX_ALIGNMENTS (SAMTOOLS_SORT.out.bam) - SAMTOOLS_INDEX_ALIGNMENTS.out.bai.dump(tag: 'BWAMETH/SAMTOOLS_INDEX_ALIGNMENTS: bai') - - ch_versions = ch_versions.mix(SAMTOOLS_INDEX_ALIGNMENTS.out.versions) - - /* - * Run samtools flagstat and samtools stats - */ - SAMTOOLS_FLAGSTAT(BWAMETH_ALIGN.out.bam.join(SAMTOOLS_INDEX_ALIGNMENTS.out.bai)) - SAMTOOLS_FLAGSTAT.out.flagstat.dump(tag: 'BWAMETH/SAMTOOLS_FLAGSTAT: flagstat') - - SAMTOOLS_STATS( - BWAMETH_ALIGN.out.bam.join(SAMTOOLS_INDEX_ALIGNMENTS.out.bai), - [[:],[]] - ) - SAMTOOLS_STATS.out.stats.dump(tag: 'BWAMETH/SAMTOOLS_STATS: flagstat') - - ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions) - ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) - - if (skip_deduplication) { - alignments = SAMTOOLS_SORT.out.bam - bam_index = SAMTOOLS_INDEX_ALIGNMENTS.out.bai - picard_metrics = Channel.empty() - picard_version = Channel.empty() - } else { - /* - * Run Picard MarkDuplicates - */ - PICARD_MARKDUPLICATES ( - SAMTOOLS_SORT.out.bam, - fasta, - fasta_index.map{ index -> [[:], index]}, - ) - PICARD_MARKDUPLICATES.out.bam.dump(tag: 'BWAMETH/PICARD_MARKDUPLICATES: bam') - /* - * Run samtools index on deduplicated alignment - */ - SAMTOOLS_INDEX_DEDUPLICATED (PICARD_MARKDUPLICATES.out.bam) - - alignments = PICARD_MARKDUPLICATES.out.bam - bam_index = SAMTOOLS_INDEX_DEDUPLICATED.out.bai - picard_metrics = PICARD_MARKDUPLICATES.out.metrics - picard_version = PICARD_MARKDUPLICATES.out.versions - ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions) - } - - - /* - * Extract per-base methylation and plot methylation bias - */ - - METHYLDACKEL_EXTRACT( - alignments.join(bam_index), - fasta.map{ meta, fasta_file -> [fasta_file]}, - fasta_index - ) - METHYLDACKEL_EXTRACT.out.bedgraph.dump(tag: 'BWAMETH/METHYLDACKEL_EXTRACT: bedgraph') - METHYLDACKEL_EXTRACT.out.methylkit.dump(tag: 'BWAMETH/METHYLDACKEL_EXTRACT: methylkit') - - METHYLDACKEL_MBIAS( - alignments.join(bam_index), - fasta.map{ meta, fasta_file -> [fasta_file]}, - fasta_index - ) - METHYLDACKEL_MBIAS.out.txt.dump(tag: 'BWAMETH/METHYLDACKEL_MBIAS: txt') - - ch_versions = ch_versions.mix(METHYLDACKEL_EXTRACT.out.versions) - ch_versions = ch_versions.mix(METHYLDACKEL_MBIAS.out.versions) - - /* - * Collect MultiQC inputs - */ - picard_metrics.collect{ it[1] } - .mix(SAMTOOLS_FLAGSTAT.out.flagstat.collect{ it[1] }) - .mix(SAMTOOLS_STATS.out.stats.collect{ it[1] }) - .mix(METHYLDACKEL_EXTRACT.out.bedgraph.collect{ it[1] }) - .mix(METHYLDACKEL_MBIAS.out.txt.collect{ it[1] }) - .set{ multiqc_files } - - emit: - bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] ## sorted, non-deduplicated (raw) BAM from aligner - dedup = alignments // channel: [ val(meta), [ bam ] ] ## sorted, possibly deduplicated BAM - mqc = multiqc_files // path: *{html,txt} - versions = ch_versions // path: *.version.txt -} diff --git a/subworkflows/local/bwameth/tests/main.nf.test b/subworkflows/local/bwameth/tests/main.nf.test deleted file mode 100644 index 21aadf8a..00000000 --- a/subworkflows/local/bwameth/tests/main.nf.test +++ /dev/null @@ -1,68 +0,0 @@ -nextflow_workflow { - - name "Test Workflow BWAMETH" - script "../main.nf" - workflow "BWAMETH" - config "../nextflow.config" - - setup { - run("UNTAR") { - script "../../../../modules/nf-core/untar/main.nf" - process { - """ - input[0] = [ - [:], - file(params.pipelines_testdata_base_path + 'reference/Bwameth_Index.tar.gz', checkIfExists: true) - ] - """ - } - } - } - - test("Bwameth | save_reference") { - - when { - params { - aligner = "bwameth" - publish_dir_mode = 'copy' - outdir = "results" - save_reference = true - save_align_intermeds = false - min_depth = 0 - comprehensive = false - ignore_flags = false - methyl_kit = false - skip_deduplication = false - } - workflow { - """ - input[0] = Channel.of([ - [ id:'test', single_end:true ], - file(params.pipelines_testdata_base_path + 'testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) - ]) - input[1] = UNTAR.out.untar - input[2] = Channel.of([ - [:], - file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) - ]) - input[3] = Channel.of(file(params.pipelines_testdata_base_path + 'reference/genome.fa.fai', checkIfExists: true)) - input[4] = params.skip_deduplication - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.bam.collect { bam(it[1]).getReadsMD5() }, - workflow.out.dedup.collect { bam(it[1]).getReadsMD5() }, - //workflow.out.mqc, - workflow.out.versions - ).match() } - ) - } - - } - -} diff --git a/subworkflows/local/bwameth/tests/main.nf.test.snap b/subworkflows/local/bwameth/tests/main.nf.test.snap deleted file mode 100644 index 3834e919..00000000 --- a/subworkflows/local/bwameth/tests/main.nf.test.snap +++ /dev/null @@ -1,27 +0,0 @@ -{ - "Bwameth | save_reference": { - "content": [ - [ - "37ec1c6338cc3fee7ab1cb2d48dba38" - ], - [ - "37ec1c6338cc3fee7ab1cb2d48dba38" - ], - [ - "versions.yml:md5,0906211fa5d0f6fd287c24407a882ae6", - "versions.yml:md5,204d3bc1f6fff3c1f7ea1f014f256fd7", - "versions.yml:md5,2b54b53cdedbbd547bc6bc3623dcc622", - "versions.yml:md5,38a8061118fdcb6215a31e60419df107", - "versions.yml:md5,5e8c932b160898dbcf29469f4ea6c978", - "versions.yml:md5,88592f164662fc6e5389899dbf472f53", - "versions.yml:md5,b935a799534fa7094fe81a723df04ecf", - "versions.yml:md5,c3658cdda0f57c6d7f0c57e820921eb4" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-21T18:23:18.006459111" - } -} \ No newline at end of file diff --git a/subworkflows/local/prepare_genome/nextflow.config b/subworkflows/local/prepare_genome/nextflow.config deleted file mode 100644 index 39f3f167..00000000 --- a/subworkflows/local/prepare_genome/nextflow.config +++ /dev/null @@ -1,4 +0,0 @@ - -includeConfig "../../../modules/nf-core/bismark/genomepreparation/nextflow.config" -includeConfig "../../../modules/nf-core/samtools/faidx/nextflow.config" -includeConfig "../../../modules/nf-core/bwameth/index/nextflow.config" diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test b/subworkflows/local/prepare_genome/tests/main.nf.test deleted file mode 100644 index c7f20b6a..00000000 --- a/subworkflows/local/prepare_genome/tests/main.nf.test +++ /dev/null @@ -1,105 +0,0 @@ -nextflow_workflow { - - name "Test Workflow PREPARE_GENOME" - script "../main.nf" - workflow "PREPARE_GENOME" - config "../nextflow.config" - - test("Generate Bismark Index (bowtie2)") { - - when { - params { - aligner = "bismark" - publish_dir_mode = copy - save_reference = false - slamseq = false - } - workflow { - """ - input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta - input[1] = [] // fasta_index - input[2] = [] // bismark_index - input[3] = [] // bwameth_index - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.fasta, - workflow.out.bismark_index, - workflow.out.versions - ).match() } - ) - } - - } - - test("Generate Bismark Index (hisat2)") { - - when { - params { - aligner = "bismark_hisat" - publish_dir_mode = copy - save_reference = false - slamseq = false - } - workflow { - """ - input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta - input[1] = [] // fasta_index - input[2] = [] // bismark_index - input[3] = [] // bwameth_index - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.fasta, - workflow.out.bismark_index, - workflow.out.versions - ).match() } - ) - } - - } - - test("Generate Bwameth Index") { - - when { - params { - aligner = "bwameth" - publish_dir_mode = copy - save_reference = false - slamseq = false - } - workflow { - """ - input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fa', checkIfExists: true) // fasta - input[1] = [] // fasta_index - input[2] = [] // bismark_index - input[3] = [] // bwameth_index - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert snapshot( - workflow.out.fasta, - workflow.out.fasta_index, - workflow.out.bwameth_index, - workflow.out.versions - ).match() } - ) - } - - } - -} diff --git a/subworkflows/local/prepare_genome/tests/main.nf.test.snap b/subworkflows/local/prepare_genome/tests/main.nf.test.snap deleted file mode 100644 index 73d4db88..00000000 --- a/subworkflows/local/prepare_genome/tests/main.nf.test.snap +++ /dev/null @@ -1,143 +0,0 @@ -{ - "Generate Bismark Index (hisat2)": { - "content": [ - [ - [ - { - - }, - "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" - ] - ], - [ - [ - { - - }, - [ - [ - [ - "BS_CT.1.ht2:md5,273c7686fc1dc7d93e36433592367f81", - "BS_CT.2.ht2:md5,752a03fc364115fc910e5a28ae154382", - "BS_CT.3.ht2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_CT.4.ht2:md5,02b3d1855a67fd9cbb4c411406a22fde", - "BS_CT.5.ht2:md5,d117de4c2c910a1ae7f0459c11ba6018", - "BS_CT.6.ht2:md5,4097a785a8d1ca92489d83b4c613a50b", - "BS_CT.7.ht2:md5,9013eccd91ad614d7893c739275a394f", - "BS_CT.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb", - "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" - ], - [ - "BS_GA.1.ht2:md5,c2b02b7987f4ac0578332204678674cd", - "BS_GA.2.ht2:md5,579241d95941538b2e75bbdb6cfaa73d", - "BS_GA.3.ht2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_GA.4.ht2:md5,6b64fa496ffa2af2af235e1c87f06a25", - "BS_GA.5.ht2:md5,43aa1c78c6ec18c4165cf25159578fee", - "BS_GA.6.ht2:md5,2dc0f049d7d0f2a51822df8b195dce41", - "BS_GA.7.ht2:md5,9013eccd91ad614d7893c739275a394f", - "BS_GA.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb", - "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" - ] - ] - ] - ] - ], - [ - "versions.yml:md5,8e4e91d03b368e548eeafee8dd263e70" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-20T15:44:14.403574883" - }, - "Generate Bwameth Index": { - "content": [ - [ - [ - { - - }, - "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" - ] - ], - [ - "genome.fa.fai:md5,84f5b44c25877ac58b154706cc8bc451" - ], - [ - [ - { - - }, - [ - "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b", - "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3", - "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110", - "genome.fa.bwameth.c2t.bwt:md5,4646f8ae6bd523b7f4106bbd32eff95e", - "genome.fa.bwameth.c2t.pac:md5,a662d7add09698e25c8152fd2306ec66", - "genome.fa.bwameth.c2t.sa:md5,4a1e905b828396a1909669bc9c573d8d" - ] - ] - ], - [ - "versions.yml:md5,7303f194674b485c6914e28422822a12", - "versions.yml:md5,cb3f3b6e54f9a7b3b6d4f5f875e89442" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-20T11:27:38.06274051" - }, - "Generate Bismark Index (bowtie2)": { - "content": [ - [ - [ - { - - }, - "/nf-core/test-datasets/raw/methylseq/reference/genome.fa" - ] - ], - [ - [ - { - - }, - [ - [ - [ - "BS_CT.1.bt2:md5,d53bef7d951c7d08e327944581c911eb", - "BS_CT.2.bt2:md5,752a03fc364115fc910e5a28ae154382", - "BS_CT.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_CT.4.bt2:md5,02b3d1855a67fd9cbb4c411406a22fde", - "BS_CT.rev.1.bt2:md5,52ae603fff473b3b25eecd36c533edb9", - "BS_CT.rev.2.bt2:md5,0e290e05f7dae065cae54e29ed97afe5", - "genome_mfa.CT_conversion.fa:md5,4dd181b65f1f3549f4132c9a3759eee8" - ], - [ - "BS_GA.1.bt2:md5,9aff51b1712758b891b0c427a988977f", - "BS_GA.2.bt2:md5,579241d95941538b2e75bbdb6cfaa73d", - "BS_GA.3.bt2:md5,b41e72eefad74e8ede411c78a5bd5dee", - "BS_GA.4.bt2:md5,6b64fa496ffa2af2af235e1c87f06a25", - "BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd", - "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49", - "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f" - ] - ] - ] - ] - ], - [ - "versions.yml:md5,8e4e91d03b368e548eeafee8dd263e70" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-20T11:27:14.196959225" - } -} \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf b/subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf index f242fc0a..a7be443a 100644 --- a/subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_methylseq_pipeline/main.nf @@ -16,9 +16,6 @@ include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' - - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -118,6 +115,7 @@ workflow PIPELINE_COMPLETION { main: summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") + def multiqc_reports = multiqc_report.toList() // // Completion email and summary @@ -131,7 +129,7 @@ workflow PIPELINE_COMPLETION { plaintext_email, outdir, monochrome_logs, - multiqc_report.toList() + multiqc_reports.getVal(), ) } @@ -233,7 +231,7 @@ def toolBibliographyText() { } def methodsDescriptionText(mqc_methods_yaml) { - // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file + // Convert to a named map so can be used as with familiar NXF ${workflow} variable syntax in the MultiQC YML file def meta = [:] meta.workflow = workflow.toMap() meta["manifest_map"] = workflow.manifest.toMap() diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf similarity index 54% rename from subworkflows/local/prepare_genome/main.nf rename to subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf index 8f8523a1..4dd21888 100644 --- a/subworkflows/local/prepare_genome/main.nf +++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/main.nf @@ -1,35 +1,34 @@ -// -// Prepare reference genome files -// - include { UNTAR } from '../../../modules/nf-core/untar/main' include { GUNZIP } from '../../../modules/nf-core/gunzip/main' include { BISMARK_GENOMEPREPARATION } from '../../../modules/nf-core/bismark/genomepreparation/main' include { BWAMETH_INDEX } from '../../../modules/nf-core/bwameth/index/main' include { SAMTOOLS_FAIDX } from '../../../modules/nf-core/samtools/faidx/main' -workflow PREPARE_GENOME { +workflow FASTA_INDEX_BISMARK_BWAMETH { + take: - fasta // file: /path/to/genome.fasta - fasta_index // file: /path/to/genome.fasta.fai - bismark_index // directory: /path/to/bismark/index/ - bwameth_index // directory: /path/to/bwameth/index/ + fasta // channel: [ val(meta), [ fasta ] ] + fasta_index // channel: [ val(meta), [ fasta index ] ] + bismark_index // channel: [ val(meta), [ bismark index ] ] + bwameth_index // channel: [ val(meta), [ bwameth index ] ] main: - ch_versions = Channel.empty() + ch_fasta = Channel.empty() ch_fasta_index = Channel.empty() ch_bismark_index = Channel.empty() ch_bwameth_index = Channel.empty() + ch_versions = Channel.empty() - // FASTA, if supplied - if (fasta.endsWith('.gz')) { - ch_fasta = GUNZIP ([ [:], file(fasta, checkIfExists: true) ]).gunzip.map { it[1] } + if (fasta.toString().endsWith('.gz')) { + GUNZIP ( + [ [:], file(fasta, checkIfExists: true) ] + ) + ch_fasta = GUNZIP.out.gunzip ch_versions = ch_versions.mix(GUNZIP.out.versions) } else { ch_fasta = Channel.value([[:], file(fasta, checkIfExists: true)]) } - ch_fasta.dump(tag: 'PREPARE_GENOME: ch_fasta') // Aligner: bismark or bismark_hisat if( params.aligner =~ /bismark/ ){ @@ -37,46 +36,44 @@ workflow PREPARE_GENOME { * Generate bismark index if not supplied */ if (bismark_index) { - if (bismark_index.endsWith('.gz')) { - ch_bismark_index = UNTAR ([ [:], file(bismark_index) ]).untar - ch_bismark_index.dump(tag: 'PREPARE_GENOME/UNTAR: ch_bismark_index') - + if (bismark_index.toString().endsWith('.gz')) { + UNTAR ( + [ [:], file(bismark_index, checkIfExists: true) ] + ) + ch_bismark_index = UNTAR.out.untar ch_versions = ch_versions.mix(UNTAR.out.versions) } else { ch_bismark_index = Channel.value([[:], file(bismark_index, checkIfExists: true)]) - ch_bismark_index.dump(tag: 'PREPARE_GENOME: ch_bismark_index') } } else { - BISMARK_GENOMEPREPARATION(ch_fasta) - + BISMARK_GENOMEPREPARATION ( + ch_fasta + ) ch_bismark_index = BISMARK_GENOMEPREPARATION.out.index - ch_bismark_index.dump(tag: 'PREPARE_GENOME: ch_bismark_index') - ch_versions = ch_versions.mix(BISMARK_GENOMEPREPARATION.out.versions) } - } + // Aligner: bwameth else if ( params.aligner == 'bwameth' ){ /* * Generate bwameth index if not supplied */ if (bwameth_index) { - if (bwameth_index.endsWith('.tar.gz')) { - ch_bwameth_index = UNTAR ([ [:], file(bwameth_index, checkIfExists: true) ]).untar - ch_bwameth_index.dump(tag: 'PREPARE_GENOME/UNTAR: ch_bwameth_index') - + if (bwameth_index.toString().endsWith('.gz')) { + UNTAR ( + [ [:], file(bwameth_index, checkIfExists: true) ] + ) + ch_bwameth_index = UNTAR.out.untar ch_versions = ch_versions.mix(UNTAR.out.versions) } else { ch_bwameth_index = Channel.value([[:], file(bwameth_index, checkIfExists: true)]) - ch_bwameth_index.dump(tag: 'PREPARE_GENOME: ch_bwameth_index') } } else { - BWAMETH_INDEX(ch_fasta) - + BWAMETH_INDEX ( + ch_fasta + ) ch_bwameth_index = BWAMETH_INDEX.out.index - ch_bwameth_index.dump(tag: 'PREPARE_GENOME: ch_bwameth_index') - ch_versions = ch_versions.mix(BWAMETH_INDEX.out.versions) } @@ -85,24 +82,21 @@ workflow PREPARE_GENOME { */ if (fasta_index) { ch_fasta_index = Channel.value(file(fasta_index, checkIfExists: true)) - ch_fasta_index.dump(tag: 'PREPARE_GENOME: ch_fasta_index') } else { SAMTOOLS_FAIDX( ch_fasta, [[:], []] ) - ch_fasta_index = SAMTOOLS_FAIDX.out.fai.map{ return(it[1])} - ch_fasta_index.dump(tag: 'PREPARE_GENOME: ch_fasta_index') - + ch_fasta_index = SAMTOOLS_FAIDX.out.fai ch_versions = ch_versions.mix(SAMTOOLS_FAIDX.out.versions) } } emit: - fasta = ch_fasta // channel: path(genome.fasta) - bismark_index = ch_bismark_index // channel: path(genome.fasta) - bwameth_index = ch_bwameth_index // channel: path(genome.fasta) - fasta_index = ch_fasta_index // channel: path(genome.fasta) - versions = ch_versions // channel: [ versions.yml ] - + fasta = ch_fasta // channel: [ val(meta), [ fasta ] ] + fasta_index = ch_fasta_index // channel: [ val(meta), [ fasta index ] ] + bismark_index = ch_bismark_index // channel: [ val(meta), [ bismark index ] ] + bwameth_index = ch_bwameth_index // channel: [ val(meta), [ bwameth index ] ] + versions = ch_versions // channel: [ versions.yml ] } + diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml b/subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml new file mode 100644 index 00000000..55854429 --- /dev/null +++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/meta.yml @@ -0,0 +1,72 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "fasta_index_bismark_bwameth" +description: Generate index files from reference fasta for bismark and bwameth +keywords: + - bismark + - bwameth + - prepare genome + - index +components: + - untar + - gunzip + - bismark/genomepreparation + - bwameth/index + - samtools/faidx +input: + - fasta: + type: file + description: | + Reference genome + Structure: [ val(meta), path(fasta) ] + pattern: "*.{fa/fa.gz}" + - fasta_index: + type: file + description: | + Reference genome index file + Structure: [ val(meta), path(fasta) ] + pattern: "*.fai" + - bismark_index: + type: file + description: | + Bismark genome index files + Structure: [ val(meta), path(bismark_index) ] + - bwameth_index: + type: file + description: | + Bwameth genome index files + Structure: [ val(meta), path(bwameth_index) ] +output: + - fasta: + type: file + description: | + Reference genome + Structure: [ val(meta), path(fasta) ] + pattern: "*.fa" + - fasta_index: + type: file + description: | + Reference genome index file + Structure: [ val(meta), path(fasta) ] + pattern: "*.fai" + - bismark_index: + type: file + description: | + Bismark genome index files + Structure: [ val(meta), path(bismark_index) ] + pattern: "BismarkIndex" + - bwameth_index: + type: file + description: | + Bwameth genome index files + Structure: [ val(meta), path(bwameth_index) ] + pattern: "index" + - versions: + type: file + description: | + File containing software versions + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@sateeshperi" +maintainers: + - "@sateeshperi" diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test new file mode 100644 index 00000000..3219ea6d --- /dev/null +++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/main.nf.test @@ -0,0 +1,227 @@ +nextflow_workflow { + + name "Test Subworkflow FASTA_INDEX_BISMARK_BWAMETH" + script "../main.nf" + workflow "FASTA_INDEX_BISMARK_BWAMETH" + config "./nextflow.config" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/fasta_index_bismark_bwameth" + tag "untar" + tag "gunzip" + tag "bismark/genomepreparation" + tag "bwameth/index" + tag "samtools/faidx" + + test("Params: bismark | download bismark index (bowtie2)") { + + when { + params { + aligner = "bismark" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = [] // fasta_index + input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz', checkIfExists: true) + input[3] = [] // bwameth_index + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark | generate bismark index (bowtie2)") { + + when { + params { + aligner = "bismark" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = [] // fasta_index + input[2] = [] // bismark_index + input[3] = [] // bwameth_index + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark_hisat | download bismark index (hisat2)") { + + when { + params { + aligner = "bismark_hisat" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = [] // fasta_index + input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true) + input[3] = [] // bwameth_index + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark_hisat | generate bismark index (hisat2)") { + + when { + params { + aligner = "bismark_hisat" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = [] // fasta_index + input[2] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true) + input[3] = [] // bwameth_index + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bwameth | download fasta index | download bwameth index") { + + when { + params { + aligner = "bwameth" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true) + input[2] = [] // bismark index + input[3] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bwameth | generate fasta index | download bwameth index") { + + when { + params { + aligner = "bwameth" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = [] //fasta index + input[2] = [] // bismark index + input[3] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bwameth | generate fasta index | generate bwameth index") { + + when { + params { + aligner = "bwameth" + } + workflow { + """ + input[0] = file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.gz', checkIfExists: true) + input[1] = [] // fasta_index + input[2] = [] // bismark index + input[3] = [] // bwameth index + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.fasta, + workflow.out.fasta_index, + workflow.out.bismark_index, + workflow.out.bwameth_index, + workflow.out.versions + ).match() } + ) + } + } + +} diff --git 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"versions.yml:md5,90950cf3155e6a77273de11ebb93a541", + "versions.yml:md5,dc24c245324a3b8a8328f1ed6abd3f7c" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-11-26T16:25:20.094964567" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/nextflow.config b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/nextflow.config new file mode 100644 index 00000000..ba4fa6f6 --- /dev/null +++ b/subworkflows/nf-core/fasta_index_bismark_bwameth/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: BISMARK_GENOMEPREPARATION { + ext.args = { params.aligner == 'bismark_hisat' ? ' --hisat2' : ' --bowtie2' } + } +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf b/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf new file mode 100644 index 00000000..e5f2ffe5 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf @@ -0,0 +1,154 @@ +include { BISMARK_ALIGN } from '../../../modules/nf-core/bismark/align/main' +include { BISMARK_DEDUPLICATE } from '../../../modules/nf-core/bismark/deduplicate/main' +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX } from '../../../modules/nf-core/samtools/index/main' +include { BISMARK_METHYLATIONEXTRACTOR } from '../../../modules/nf-core/bismark/methylationextractor/main' +include { BISMARK_COVERAGE2CYTOSINE } from '../../../modules/nf-core/bismark/coverage2cytosine/main' +include { BISMARK_REPORT } from '../../../modules/nf-core/bismark/report/main' +include { BISMARK_SUMMARY } from '../../../modules/nf-core/bismark/summary/main' + +workflow FASTQ_ALIGN_DEDUP_BISMARK { + + take: + ch_reads // channel: [ val(meta), [ reads ] ] + ch_fasta // channel: [ val(meta), [ fasta ] ] + ch_bismark_index // channel: [ val(meta), [ bismark index ] ] + skip_deduplication // boolean: whether to deduplicate alignments + cytosine_report // boolean: whether the run coverage2cytosine + + main: + ch_alignments = Channel.empty() + ch_alignment_reports = Channel.empty() + ch_methylation_bedgraph = Channel.empty() + ch_methylation_calls = Channel.empty() + ch_methylation_coverage = Channel.empty() + ch_methylation_report = Channel.empty() + ch_methylation_mbias = Channel.empty() + ch_coverage2cytosine_coverage = Channel.empty() + ch_coverage2cytosine_report = Channel.empty() + ch_coverage2cytosine_summary = Channel.empty() + ch_bismark_report = Channel.empty() + ch_bismark_summary = Channel.empty() + ch_multiqc_files = Channel.empty() + ch_versions = Channel.empty() + + /* + * Align with bismark + */ + BISMARK_ALIGN ( + ch_reads, + ch_fasta, + ch_bismark_index + ) + ch_alignments = BISMARK_ALIGN.out.bam + ch_alignment_reports = BISMARK_ALIGN.out.report.map{ meta, report -> [ meta, report, [] ] } + ch_versions = ch_versions.mix(BISMARK_ALIGN.out.versions) + + if (!skip_deduplication) { + /* + * Run deduplicate_bismark + */ + BISMARK_DEDUPLICATE ( + BISMARK_ALIGN.out.bam + ) + ch_alignments = BISMARK_DEDUPLICATE.out.bam + ch_alignment_reports = BISMARK_ALIGN.out.report.join(BISMARK_DEDUPLICATE.out.report) + ch_versions = ch_versions.mix(BISMARK_DEDUPLICATE.out.versions) + } + + /* + * MODULE: Run samtools sort on aligned or deduplicated bam + */ + SAMTOOLS_SORT ( + ch_alignments, + [[:],[]] // [ [meta], [fasta]] + ) + ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) + + /* + * MODULE: Run samtools index on aligned or deduplicated bam + */ + SAMTOOLS_INDEX ( + SAMTOOLS_SORT.out.bam + ) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions) + + /* + * Run bismark_methylation_extractor + */ + BISMARK_METHYLATIONEXTRACTOR ( + ch_alignments, + ch_bismark_index + ) + ch_methylation_bedgraph = BISMARK_METHYLATIONEXTRACTOR.out.bedgraph + ch_methylation_calls = BISMARK_METHYLATIONEXTRACTOR.out.methylation_calls + ch_methylation_coverage = BISMARK_METHYLATIONEXTRACTOR.out.coverage + ch_methylation_report = BISMARK_METHYLATIONEXTRACTOR.out.report + ch_methylation_mbias = BISMARK_METHYLATIONEXTRACTOR.out.mbias + ch_versions = ch_versions.mix(BISMARK_METHYLATIONEXTRACTOR.out.versions) + + /* + * Run bismark coverage2cytosine + */ + if (cytosine_report) { + BISMARK_COVERAGE2CYTOSINE ( + ch_methylation_coverage, + ch_fasta, + ch_bismark_index + ) + ch_coverage2cytosine_coverage = BISMARK_COVERAGE2CYTOSINE.out.coverage + ch_coverage2cytosine_report = BISMARK_COVERAGE2CYTOSINE.out.report + ch_coverage2cytosine_summary = BISMARK_COVERAGE2CYTOSINE.out.summary + ch_versions = ch_versions.mix(BISMARK_COVERAGE2CYTOSINE.out.versions) + } + + /* + * Generate bismark sample reports + */ + BISMARK_REPORT ( + ch_alignment_reports + .join(ch_methylation_report) + .join(ch_methylation_mbias) + ) + ch_bismark_report = BISMARK_REPORT.out.report + ch_versions = ch_versions.mix(BISMARK_REPORT.out.versions) + + /* + * Generate bismark summary report + */ + BISMARK_SUMMARY ( + BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam.name }, + ch_alignment_reports.collect{ meta, align_report, dedup_report -> align_report }, + ch_alignment_reports.collect{ meta, align_report, dedup_report -> dedup_report }.ifEmpty([]), + ch_methylation_report.collect{ meta, report -> report }, + ch_methylation_mbias.collect{ meta, mbias -> mbias } + ) + ch_bismark_summary = BISMARK_SUMMARY.out.summary + ch_versions = ch_versions.mix(BISMARK_SUMMARY.out.versions) + + /* + * Collect MultiQC inputs + */ + ch_multiqc_files = ch_bismark_summary + .mix(ch_alignment_reports.collect{ meta, align_report, dedup_report -> align_report }) + .mix(ch_alignment_reports.collect{ meta, align_report, dedup_report -> dedup_report }) + .mix(ch_methylation_report.collect{ meta, report -> report }) + .mix(ch_methylation_mbias.collect{ meta, mbias -> mbias }) + .mix(ch_bismark_report.collect{ meta, report -> report }) + + emit: + bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ] + bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ] + coverage2cytosine_coverage = ch_coverage2cytosine_coverage // channel: [ val(meta), [ coverage ] ] + coverage2cytosine_report = ch_coverage2cytosine_report // channel: [ val(meta), [ report ] ] + coverage2cytosine_summary = ch_coverage2cytosine_summary // channel: [ val(meta), [ summary ] ] + methylation_bedgraph = ch_methylation_bedgraph // channel: [ val(meta), [ bedgraph ] ] + methylation_calls = ch_methylation_calls // channel: [ val(meta), [ methylation_calls ] ] + methylation_coverage = ch_methylation_coverage // channel: [ val(meta), [ coverage ] ] + methylation_report = ch_methylation_report // channel: [ val(meta), [ report ] ] + methylation_mbias = ch_methylation_mbias // channel: [ val(meta), [ mbias ] ] + bismark_report = ch_bismark_report // channel: [ val(meta), [ report ] ] + bismark_summary = ch_bismark_summary // channel: [ val(meta), [ summary ] ] + multiqc = ch_multiqc_files // path: *{html,txt} + versions = ch_versions // path: *.version.txt +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml b/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml new file mode 100644 index 00000000..7622b98e --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml @@ -0,0 +1,136 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "fastq_align_dedup_bismark" +description: Align BS-Seq reads to a reference genome using bismark, deduplicate and sort +keywords: + - bismark + - 3-letter genome + - map + - methylation + - 5mC + - methylseq + - bisulphite + - bisulfite + - bam +components: + - bismark/align + - samtools/sort + - samtools/index + - bismark/deduplicate + - bismark/methylationextractor + - bismark/coverage2cytosine + - bismark/report + - bismark/summary +input: + - ch_reads: + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + Structure: [ val(meta), [ path(reads) ] ] + pattern: "*.{fastq,fastq.gz}" + - ch_fasta: + type: file + description: | + Structure: [ val(meta), path(fasta) ] + pattern: "*.{fa,fa.gz}" + - ch_bismark_index: + description: | + Bismark genome index files + Structure: [ val(meta), path(index) ] + pattern: "BismarkIndex" + - skip_deduplication: + type: boolean + description: | + Skip deduplication of aligned reads + - cytosine_report: + type: boolean + description: | + Produce coverage2cytosine reports that relates methylation calls back to genomic cytosine contexts +output: + - bam: + type: file + description: | + Channel containing aligned or deduplicated BAM files. + Structure: [ val(meta), path(bam) ] + pattern: "*.bam" + - bai: + type: file + description: | + Channel containing aligned or deduplicated BAM index files. + Structure: [ val(meta), path(bam.bai) ] + pattern: "*.bai" + - coverage2cytosine_coverage: + type: file + description: | + Channel containing coverage information from coverage2cytosine. + Structure: [ val(meta), path(coverage.txt) ] + pattern: "*.cov.gz" + - coverage2cytosine_report: + type: file + description: | + Channel containing report from coverage2cytosine summarizing cytosine methylation coverage. + Structure: [ val(meta), path(report.txt) ] + pattern: "*report.txt.gz" + - coverage2cytosine_summary: + type: file + description: | + Channel containing summary information from coverage2cytosine. + Structure: [ val(meta), path(summary.txt) ] + pattern: "*cytosine_context_summary.txt" + - methylation_bedgraph: + type: file + description: | + Channel containing methylation data in bedGraph format. + Structure: [ val(meta), path(methylation.bedgraph) ] + pattern: "*.bedGraph.gz" + - methylation_calls: + type: file + description: | + Channel containing methylation call data. + Structure: [ val(meta), path(calls.txt) ] + pattern: "*.txt.gz" + - methylation_coverage: + type: file + description: | + Channel containing methylation coverage data. + Structure: [ val(meta), path(coverage.txt) ] + pattern: "*.cov.gz" + - methylation_report: + type: file + description: | + Channel containing methylation report detailing methylation patterns. + Structure: [ val(meta), path(report.txt) ] + pattern: "*_splitting_report.txt" + - methylation_mbias: + type: file + description: | + Channel containing M-bias report showing methylation bias across read positions. + Structure: [ val(meta), path(mbias.txt) ] + pattern: "*.M-bias.txt" + - bismark_report: + type: file + description: | + Channel containing Bismark report with mapping and methylation statistics. + Structure: [ val(meta), path(bismark_report.txt) ] + pattern: "*report.{html,txt}" + - bismark_summary: + type: file + description: | + Channel containing Bismark summary report. + Structure: [ val(meta), path(bismark_summary.txt) ] + pattern: "*report.{html,txt}" + - multiqc: + type: file + description: | + Channel containing MultiQC report aggregating results across samples. + Structure: [ val(meta), path(multiqc_report.html) ] + pattern: "*.html" + - versions: + type: file + description: | + File containing software versions. + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@sateeshperi" +maintainers: + - "@sateeshperi" diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test new file mode 100644 index 00000000..27bf692a --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test @@ -0,0 +1,440 @@ +nextflow_workflow { + + name "Test Subworkflow FASTQ_ALIGN_DEDUP_BISMARK" + script "../main.nf" + workflow "FASTQ_ALIGN_DEDUP_BISMARK" + config "./nextflow.config" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/fastq_align_dedup_bismark" + tag "bismark/align" + tag "samtools/sort" + tag "samtools/index" + tag "bismark/deduplicate" + tag "bismark/methylationextractor" + tag "bismark/coverage2cytosine" + tag "bismark/report" + tag "bismark/summary" + tag "untar" + + setup { + run("UNTAR", alias: "BOWTIE2") { + script "../../../../modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz', checkIfExists: true) + ] + """ + } + } + + run("UNTAR", alias: "HISAT2") { + script "../../../../modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + test("Params: bismark single-end | default") { + + when { + params { + aligner = "bismark" + cytosine_report = false + skip_deduplication = false + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = BOWTIE2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark paired-end | default") { + + when { + params { + aligner = "bismark" + cytosine_report = false + skip_deduplication = false + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = BOWTIE2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark paired-end | skip_deduplication") { + + when { + params { + aligner = "bismark" + skip_deduplication = true + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = BOWTIE2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark paired-end | cytosine_report") { + + when { + params { + aligner = "bismark" + cytosine_report = true + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = BOWTIE2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark_hisat single-end | default") { + + when { + params { + aligner = "bismark_hisat" + cytosine_report = false + skip_deduplication = false + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = HISAT2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark_hisat paired-end | default") { + + when { + params { + aligner = "bismark_hisat" + cytosine_report = false + skip_deduplication = false + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = HISAT2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark_hisat paired-end | skip_deduplication") { + + when { + params { + aligner = "bismark_hisat" + skip_deduplication = true + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = HISAT2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bismark_hisat paired-end | cytosine_report") { + + when { + params { + aligner = "bismark_hisat" + cytosine_report = true + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = HISAT2.out.untar + input[3] = params.skip_deduplication + input[4] = params.cytosine_report + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.coverage2cytosine_coverage, + workflow.out.coverage2cytosine_report, + workflow.out.coverage2cytosine_summary, + workflow.out.methylation_bedgraph, + workflow.out.methylation_calls, + workflow.out.methylation_coverage, + workflow.out.methylation_report, + workflow.out.methylation_mbias, + workflow.out.bismark_report.collect { meta, report -> file(report).name }, + workflow.out.bismark_summary[0][1], + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap new file mode 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' --hisat2' : ' --bowtie2' } + } + + withName: 'SAMTOOLS_SORT' { + ext.prefix = { "${meta.id}.sorted" } + } +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf new file mode 100644 index 00000000..c0cc67b8 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf @@ -0,0 +1,163 @@ +include { BWAMETH_ALIGN } from '../../../modules/nf-core/bwameth/align/main' +include { PARABRICKS_FQ2BAMMETH } from '../../../modules/nf-core/parabricks/fq2bammeth/main' +include { SAMTOOLS_SORT } from '../../../modules/nf-core/samtools/sort/main' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_ALIGNMENTS } from '../../../modules/nf-core/samtools/index/main' +include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/samtools/flagstat/main' +include { SAMTOOLS_STATS } from '../../../modules/nf-core/samtools/stats/main' +include { PICARD_MARKDUPLICATES } from '../../../modules/nf-core/picard/markduplicates/main' +include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_DEDUPLICATED } from '../../../modules/nf-core/samtools/index/main' +include { METHYLDACKEL_EXTRACT } from '../../../modules/nf-core/methyldackel/extract/main' +include { METHYLDACKEL_MBIAS } from '../../../modules/nf-core/methyldackel/mbias/main' + +workflow FASTQ_ALIGN_DEDUP_BWAMETH { + + take: + ch_reads // channel: [ val(meta), [ reads ] ] + ch_fasta // channel: [ val(meta), [ fasta ] ] + ch_fasta_index // channel: [ val(meta), [ fasta index ] ] + ch_bwameth_index // channel: [ val(meta), [ bwameth index ] ] + skip_deduplication // boolean: whether to deduplicate alignments + + main: + + ch_alignment = Channel.empty() + ch_alignment_index = Channel.empty() + ch_samtools_flagstat = Channel.empty() + ch_samtools_stats = Channel.empty() + ch_methydackel_extract_bedgraph = Channel.empty() + ch_methydackel_extract_methylkit = Channel.empty() + ch_methydackel_mbias = Channel.empty() + ch_picard_metrics = Channel.empty() + ch_multiqc_files = Channel.empty() + ch_versions = Channel.empty() + + /* + * Align with bwameth + */ + if (params.use_gpu) { + /* + * Align with parabricks GPU enabled fq2bammeth implementation of bwameth + */ + PARABRICKS_FQ2BAMMETH ( + ch_reads, + ch_fasta, + ch_bwameth_index, + [] // known sites + ) + ch_alignment = PARABRICKS_FQ2BAMMETH.out.bam + ch_versions = ch_versions.mix(PARABRICKS_FQ2BAMMETH.out.versions) + } else { + /* + * Align with CPU version of bwameth + */ + BWAMETH_ALIGN ( + ch_reads, + ch_fasta, + ch_bwameth_index + ) + ch_alignment = BWAMETH_ALIGN.out.bam + ch_versions = BWAMETH_ALIGN.out.versions + } + + /* + * Sort raw output BAM + */ + SAMTOOLS_SORT ( + ch_alignment, + [[:],[]] // [ [meta], [fasta]] + ) + ch_alignment = SAMTOOLS_SORT.out.bam + ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions) + + /* + * Run samtools index on alignment + */ + SAMTOOLS_INDEX_ALIGNMENTS ( + ch_alignment + ) + ch_alignment_index = SAMTOOLS_INDEX_ALIGNMENTS.out.bai + ch_versions = ch_versions.mix(SAMTOOLS_INDEX_ALIGNMENTS.out.versions) + + /* + * Run samtools flagstat + */ + SAMTOOLS_FLAGSTAT ( + ch_alignment.join(ch_alignment_index) + ) + ch_samtools_flagstat = SAMTOOLS_FLAGSTAT.out.flagstat + ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions) + + /* + * Run samtools stats + */ + SAMTOOLS_STATS ( + ch_alignment.join(ch_alignment_index), + [[:],[]] // [ [meta], [fasta]] + ) + ch_samtools_stats = SAMTOOLS_STATS.out.stats + ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions) + + if (!skip_deduplication) { + /* + * Run Picard MarkDuplicates + */ + PICARD_MARKDUPLICATES ( + ch_alignment, + ch_fasta, + ch_fasta_index + ) + /* + * Run samtools index on deduplicated alignment + */ + SAMTOOLS_INDEX_DEDUPLICATED ( + PICARD_MARKDUPLICATES.out.bam + ) + ch_alignment = PICARD_MARKDUPLICATES.out.bam + ch_alignment_index = SAMTOOLS_INDEX_DEDUPLICATED.out.bai + ch_picard_metrics = PICARD_MARKDUPLICATES.out.metrics + ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions) + ch_versions = ch_versions.mix(SAMTOOLS_INDEX_DEDUPLICATED.out.versions) + } + + /* + * Extract per-base methylation and plot methylation bias + */ + + METHYLDACKEL_EXTRACT ( + ch_alignment.join(ch_alignment_index), + ch_fasta.map{ meta, fasta_file -> fasta_file }, + ch_fasta_index.map{ meta, fasta_index -> fasta_index } + ) + ch_methydackel_extract_bedgraph = METHYLDACKEL_EXTRACT.out.bedgraph + ch_methydackel_extract_methylkit = METHYLDACKEL_EXTRACT.out.methylkit + ch_versions = ch_versions.mix(METHYLDACKEL_EXTRACT.out.versions) + + METHYLDACKEL_MBIAS ( + ch_alignment.join(ch_alignment_index), + ch_fasta.map{ meta, fasta_file -> fasta_file }, + ch_fasta_index.map{ meta, fasta_index -> fasta_index } + ) + ch_methydackel_mbias = METHYLDACKEL_MBIAS.out.txt + ch_versions = ch_versions.mix(METHYLDACKEL_MBIAS.out.versions) + + /* + * Collect MultiQC inputs + */ + ch_multiqc_files = ch_picard_metrics.collect{ meta, metrics -> metrics } + .mix(ch_samtools_flagstat.collect{ meta, flagstat -> flagstat }) + .mix(ch_samtools_stats.collect{ meta, stats -> stats }) + .mix(ch_methydackel_extract_bedgraph.collect{ meta, bedgraph -> bedgraph }) + .mix(ch_methydackel_mbias.collect{ meta, txt -> txt }) + + emit: + bam = ch_alignment // channel: [ val(meta), [ bam ] ] + bai = ch_alignment_index // channel: [ val(meta), [ bai ] ] + samtools_flagstat = ch_samtools_flagstat // channel: [ val(meta), [ flagstat ] ] + samtools_stats = ch_samtools_stats // channel: [ val(meta), [ stats ] ] + methydackel_extract_bedgraph = ch_methydackel_extract_bedgraph // channel: [ val(meta), [ bedgraph ] ] + methydackel_extract_methylkit = ch_methydackel_extract_methylkit // channel: [ val(meta), [ methylkit ] ] + methydackel_mbias = ch_methydackel_mbias // channel: [ val(meta), [ mbias ] ] + picard_metrics = ch_picard_metrics // channel: [ val(meta), [ metrics ] ] + multiqc = ch_multiqc_files // channel: [ *{html,txt} ] + versions = ch_versions // channel: [ versions.yml ] +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml b/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml new file mode 100644 index 00000000..a66ea024 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/meta.yml @@ -0,0 +1,116 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "fastq_align_dedup_bwameth" +description: Performs alignment of BS-Seq reads using bwameth or parabricks/fq2bammeth, sort and deduplicate +keywords: + - bwameth + - alignment + - 3-letter genome + - map + - methylation + - 5mC + - methylseq + - bisulphite + - bisulfite + - fastq + - bam +components: + - bwameth/align + - parabricks/fq2bammeth + - samtools/sort + - samtools/index + - samtools/flagstat + - samtools/stats + - picard/markduplicates + - samtools/index + - methyldackel/extract + - methyldackel/mbias +input: + - ch_reads: + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + Structure: [ val(meta), [ path(reads) ] ] + pattern: "*.{fastq,fastq.gz}" + - ch_fasta: + type: file + description: | + Structure: [ val(meta), path(fasta) ] + pattern: "*.{fa,fa.gz}" + - ch_fasta_index: + type: file + description: | + Structure: [ val(meta), path(fasta index) ] + - ch_bwameth_index: + description: | + Bismark genome index files + Structure: [ val(meta), path(index) ] + pattern: "BismarkIndex" + - skip_deduplication: + type: boolean + description: | + Skip deduplication of aligned reads +output: + - bam: + type: file + description: | + Channel containing BAM files + Structure: [ val(meta), path(bam) ] + pattern: "*.bam" + - bai: + type: file + description: | + Channel containing indexed BAM (BAI) files + Structure: [ val(meta), path(bai) ] + pattern: "*.bai" + - samtools_flagstat: + type: file + description: | + File containing samtools flagstat output + Structure: [ val(meta), path(flagstat) ] + pattern: "*.flagstat" + - samtools_stats: + type: file + description: | + File containing samtools stats output + Structure: [ val(meta), path(stats) ] + pattern: "*.{stats}" + - methydackel_extract_bedgraph: + type: file + description: | + bedGraph file, containing per-base methylation metrics + Structure: [ val(meta), path(bedgraph) ] + pattern: "*.bedGraph" + - methydackel_extract_methylkit: + type: file + description: | + methylKit file, containing per-base methylation metrics + Structure: [ val(meta), path(methylKit) ] + pattern: "*.methylKit" + - methydackel_mbias: + type: file + description: | + Text file containing methylation bias + Structure: [ val(meta), path(mbias) ] + pattern: "*.{txt}" + - picard_metrics: + type: file + description: | + Duplicate metrics file generated by picard + Structure: [ val(meta), path(metrics) ] + pattern: "*.{metrics.txt}" + - multiqc: + type: file + description: | + Channel containing MultiQC report aggregating results across samples. + Structure: [ val(meta), path(multiqc_report.html) ] + pattern: "*.html" + - versions: + type: file + description: | + File containing software versions + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@sateeshperi" +maintainers: + - "@sateeshperi" diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test new file mode 100644 index 00000000..b156de6b --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test @@ -0,0 +1,132 @@ +nextflow_workflow { + + name "Test Subworkflow FASTQ_ALIGN_DEDUP_BWAMETH" + script "../main.nf" + workflow "FASTQ_ALIGN_DEDUP_BWAMETH" + config "./nextflow.config" + + tag "gpu" + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/fastq_align_dedup_bwameth" + tag "bwameth/align" + tag "parabricks/fq2bammeth" + tag "samtools/sort" + tag "samtools/index" + tag "samtools/flagstat" + tag "samtools/stats" + tag "picard/markduplicates" + tag "samtools/index" + tag "methyldackel/extract" + tag "methyldackel/mbias" + tag "untar" + + setup { + run("UNTAR") { + script "../../../../modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + test("Params: parabricks/fq2bammeth single-end | use_gpu") { + + when { + params { + skip_deduplication = false + use_gpu = true + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true) + ]) + input[3] = UNTAR.out.untar + input[4] = params.skip_deduplication + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.samtools_flagstat, + workflow.out.samtools_stats, + workflow.out.methydackel_extract_bedgraph, + workflow.out.methydackel_extract_methylkit, + workflow.out.methydackel_mbias, + workflow.out.picard_metrics.collect { meta, metrics -> file(metrics).name }, + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: parabricks/fq2bammeth single-end | use_gpu | skip_deduplication") { + + when { + params { + skip_deduplication = true + use_gpu = true + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true) + ]) + input[3] = UNTAR.out.untar + input[4] = params.skip_deduplication + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.samtools_flagstat, + workflow.out.samtools_stats, + workflow.out.methydackel_extract_bedgraph, + workflow.out.methydackel_extract_methylkit, + workflow.out.methydackel_mbias, + workflow.out.picard_metrics.collect { meta, metrics -> file(metrics).name }, + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap new file mode 100644 index 00000000..a1602b30 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap @@ -0,0 +1,149 @@ +{ + "Params: parabricks/fq2bammeth single-end | use_gpu": { + "content": [ + [ + "a7f7ca7b5eb503ab58790d64a0273ed6" + ], + [ + "test.markdup.sorted.bam.bai" + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,897d500a710a56a7098172167fa71108" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,9aac964b859fda8239aa0eae16382d56" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.markdup.sorted_CpG.bedGraph:md5,f2fe02f180456f5f4922a2a8aa559fca" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81" + ] + ], + [ + "test.markdup.sorted.MarkDuplicates.metrics.txt" + ], + [ + "test.flagstat", + "test.markdup.sorted.MarkDuplicates.metrics.txt", + "test.markdup.sorted_CpG.bedGraph", + "test.mbias.txt", + "test.stats" + ], + [ + "versions.yml:md5,36bd052d24ec766084f6aa2fb8a6ae4c", + "versions.yml:md5,45239309d0c40b5f0a56eba4347f09be", + "versions.yml:md5,4a6bb9a47d944ab197c823ae0ae61092", + "versions.yml:md5,8b72c7013fa6f632d28933b60ad1f2ea", + "versions.yml:md5,a80a57d29a4d72830f033bc0326b1abf", + "versions.yml:md5,b6492c12bfae23b6e279f4abfd4780e5", + "versions.yml:md5,baba90d5bd57679b913be2abd531ae15", + "versions.yml:md5,ddbe480ff81df55c6d95f911e7b6dc8a", + "versions.yml:md5,e9602257141b65a907ad9036e8a32a83" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-17T06:56:47.211389" + }, + "Params: parabricks/fq2bammeth single-end | use_gpu | skip_deduplication": { + "content": [ + [ + "a7f7ca7b5eb503ab58790d64a0273ed6" + ], + [ + "test.sorted.bam.bai" + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,897d500a710a56a7098172167fa71108" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,9aac964b859fda8239aa0eae16382d56" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.sorted_CpG.bedGraph:md5,b0cb426020f8beb45b4e8f09b9a17bfa" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81" + ] + ], + [ + + ], + [ + "test.flagstat", + "test.mbias.txt", + "test.sorted_CpG.bedGraph", + "test.stats" + ], + [ + "versions.yml:md5,36bd052d24ec766084f6aa2fb8a6ae4c", + "versions.yml:md5,4a6bb9a47d944ab197c823ae0ae61092", + "versions.yml:md5,8b72c7013fa6f632d28933b60ad1f2ea", + "versions.yml:md5,a80a57d29a4d72830f033bc0326b1abf", + "versions.yml:md5,b6492c12bfae23b6e279f4abfd4780e5", + "versions.yml:md5,baba90d5bd57679b913be2abd531ae15", + "versions.yml:md5,e9602257141b65a907ad9036e8a32a83" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-17T06:57:34.41912" + } +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test new file mode 100644 index 00000000..6b20d545 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test @@ -0,0 +1,179 @@ +nextflow_workflow { + + name "Test Subworkflow FASTQ_ALIGN_DEDUP_BWAMETH" + script "../main.nf" + workflow "FASTQ_ALIGN_DEDUP_BWAMETH" + config "./nextflow.config" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/fastq_align_dedup_bwameth" + tag "bwameth/align" + tag "parabricks/fq2bammeth" + tag "samtools/sort" + tag "samtools/index" + tag "samtools/flagstat" + tag "samtools/stats" + tag "picard/markduplicates" + tag "samtools/index" + tag "methyldackel/extract" + tag "methyldackel/mbias" + tag "untar" + + setup { + run("UNTAR") { + script "../../../../modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + test("Params: bwameth single-end | default") { + + when { + params { + skip_deduplication = false + use_gpu = false + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true) + ]) + input[3] = UNTAR.out.untar + input[4] = params.skip_deduplication + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.samtools_flagstat, + workflow.out.samtools_stats, + workflow.out.methydackel_extract_bedgraph, + workflow.out.methydackel_extract_methylkit, + workflow.out.methydackel_mbias, + workflow.out.picard_metrics.collect { meta, metrics -> file(metrics).name }, + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bwameth paired-end | default") { + + when { + params { + skip_deduplication = false + use_gpu = false + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true) + ]) + input[3] = UNTAR.out.untar + input[4] = params.skip_deduplication + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.samtools_flagstat, + workflow.out.samtools_stats, + workflow.out.methydackel_extract_bedgraph, + workflow.out.methydackel_extract_methylkit, + workflow.out.methydackel_mbias, + workflow.out.picard_metrics.collect { meta, metrics -> file(metrics).name }, + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } + + test("Params: bwameth paired-end | skip_deduplication") { + + when { + params { + skip_deduplication = true + use_gpu = false + } + + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R1.fastq.gz', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/Ecoli_10K_methylated_R2.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) + ]) + input[2] = Channel.of([ + [:], + file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa.fai', checkIfExists: true) + ]) + input[3] = UNTAR.out.untar + input[4] = params.skip_deduplication + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, + workflow.out.bai.collect { meta, bai -> file(bai).name }, + workflow.out.samtools_flagstat, + workflow.out.samtools_stats, + workflow.out.methydackel_extract_bedgraph, + workflow.out.methydackel_extract_methylkit, + workflow.out.methydackel_mbias, + workflow.out.picard_metrics.collect { meta, metrics -> file(metrics).name }, + workflow.out.multiqc.flatten().collect { path -> file(path).name }, + workflow.out.versions + ).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap new file mode 100644 index 00000000..90c96015 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap @@ -0,0 +1,224 @@ +{ + "Params: bwameth single-end | default": { + "content": [ + [ + "37ec1c6338cc3fee7ab1cb2d48dba38" + ], + [ + "test.markdup.sorted.bam.bai" + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,897d500a710a56a7098172167fa71108" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,9aac964b859fda8239aa0eae16382d56" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.markdup.sorted_CpG.bedGraph:md5,f2fe02f180456f5f4922a2a8aa559fca" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81" + ] + ], + [ + "test.markdup.sorted.MarkDuplicates.metrics.txt" + ], + [ + "test.flagstat", + "test.markdup.sorted.MarkDuplicates.metrics.txt", + "test.markdup.sorted_CpG.bedGraph", + "test.mbias.txt", + "test.stats" + ], + [ + "versions.yml:md5,36bd052d24ec766084f6aa2fb8a6ae4c", + "versions.yml:md5,45239309d0c40b5f0a56eba4347f09be", + "versions.yml:md5,4a6bb9a47d944ab197c823ae0ae61092", + "versions.yml:md5,8b72c7013fa6f632d28933b60ad1f2ea", + "versions.yml:md5,8edf3166176c863b88ba488f8b715aa3", + "versions.yml:md5,a80a57d29a4d72830f033bc0326b1abf", + "versions.yml:md5,b6492c12bfae23b6e279f4abfd4780e5", + "versions.yml:md5,baba90d5bd57679b913be2abd531ae15", + "versions.yml:md5,ddbe480ff81df55c6d95f911e7b6dc8a" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-17T05:42:12.81856451" + }, + "Params: bwameth paired-end | skip_deduplication": { + "content": [ + [ + "cf25656fffc044f2bb7d9f1b3686ecb4" + ], + [ + "test.sorted.bam.bai" + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,4ff87d121ca174953734723938c99081" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,c753c72eb4e1c32f74afb1fbd932fe1f" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.sorted_CpG.bedGraph:md5,285e492823182f5705bf0817e2d088b8" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.mbias.txt:md5,c1fda203c1b19aca2498efe0fd4cc9e3" + ] + ], + [ + + ], + [ + "test.flagstat", + "test.mbias.txt", + "test.sorted_CpG.bedGraph", + "test.stats" + ], + [ + "versions.yml:md5,36bd052d24ec766084f6aa2fb8a6ae4c", + "versions.yml:md5,4a6bb9a47d944ab197c823ae0ae61092", + "versions.yml:md5,8b72c7013fa6f632d28933b60ad1f2ea", + "versions.yml:md5,8edf3166176c863b88ba488f8b715aa3", + "versions.yml:md5,a80a57d29a4d72830f033bc0326b1abf", + "versions.yml:md5,b6492c12bfae23b6e279f4abfd4780e5", + "versions.yml:md5,baba90d5bd57679b913be2abd531ae15" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-17T05:10:43.907134648" + }, + "Params: bwameth paired-end | default": { + "content": [ + [ + "cf25656fffc044f2bb7d9f1b3686ecb4" + ], + [ + "test.markdup.sorted.bam.bai" + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.flagstat:md5,4ff87d121ca174953734723938c99081" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.stats:md5,c753c72eb4e1c32f74afb1fbd932fe1f" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.markdup.sorted_CpG.bedGraph:md5,c6c73e5abba70ac799500f592fec5c29" + ] + ], + [ + + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test.mbias.txt:md5,c1fda203c1b19aca2498efe0fd4cc9e3" + ] + ], + [ + "test.markdup.sorted.MarkDuplicates.metrics.txt" + ], + [ + "test.flagstat", + "test.markdup.sorted.MarkDuplicates.metrics.txt", + "test.markdup.sorted_CpG.bedGraph", + "test.mbias.txt", + "test.stats" + ], + [ + "versions.yml:md5,36bd052d24ec766084f6aa2fb8a6ae4c", + "versions.yml:md5,45239309d0c40b5f0a56eba4347f09be", + "versions.yml:md5,4a6bb9a47d944ab197c823ae0ae61092", + "versions.yml:md5,8b72c7013fa6f632d28933b60ad1f2ea", + "versions.yml:md5,8edf3166176c863b88ba488f8b715aa3", + "versions.yml:md5,a80a57d29a4d72830f033bc0326b1abf", + "versions.yml:md5,b6492c12bfae23b6e279f4abfd4780e5", + "versions.yml:md5,baba90d5bd57679b913be2abd531ae15", + "versions.yml:md5,ddbe480ff81df55c6d95f911e7b6dc8a" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-17T05:42:39.183331191" + } +} diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/nextflow.config b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/nextflow.config new file mode 100644 index 00000000..55385ec0 --- /dev/null +++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/nextflow.config @@ -0,0 +1,14 @@ +process { + withName: 'PARABRICKS_FQ2BAMMETH' { + ext.args = '--low-memory' + } + + withName: 'SAMTOOLS_SORT' { + ext.prefix = { "${meta.id}.sorted" } + } + + withName: 'PICARD_MARKDUPLICATES' { + ext.args = "--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --PROGRAM_RECORD_ID 'null' --TMP_DIR tmp" + ext.prefix = { "${meta.id}.markdup.sorted" } + } +} diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 0fcbf7b3..d6e593e8 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -92,10 +92,12 @@ def checkCondaChannels() { channels = config.channels } catch (NullPointerException e) { + log.debug(e) log.warn("Could not verify conda channel configuration.") return null } catch (IOException e) { + log.debug(e) log.warn("Could not verify conda channel configuration.") return null } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test index ca964ce8..02dbf094 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test @@ -52,10 +52,12 @@ nextflow_workflow { } then { - assertAll( - { assert workflow.success }, - { assert workflow.stdout.contains("nextflow_workflow v9.9.9") } - ) + expect { + with(workflow) { + assert success + assert "nextflow_workflow v9.9.9" in stdout + } + } } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 5cb7bafe..bfd25876 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -56,21 +56,6 @@ def checkProfileProvided(nextflow_cli_args) { } } -// -// Citation string for pipeline -// -def workflowCitation() { - def temp_doi_ref = "" - def manifest_doi = workflow.manifest.doi.tokenize(",") - // Handling multiple DOIs - // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers - // Removing ` ` since the manifest.doi is a string and not a proper list - manifest_doi.each { doi_ref -> - temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" - } - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" -} - // // Generate workflow version string // @@ -150,33 +135,6 @@ def paramsSummaryMultiqc(summary_params) { return yaml_file_text } -// -// nf-core logo -// -def nfCoreLogo(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - String.format( - """\n - ${dashedLine(monochrome_logs)} - ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} - ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} - ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} - ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} - ${colors.green}`._,._,\'${colors.reset} - ${colors.purple} ${workflow.manifest.name} ${getWorkflowVersion()}${colors.reset} - ${dashedLine(monochrome_logs)} - """.stripIndent() - ) -} - -// -// Return dashed line -// -def dashedLine(monochrome_logs=true) { - def colors = logColours(monochrome_logs) as Map - return "-${colors.dim}----------------------------------------------------${colors.reset}-" -} - // // ANSII colours used for terminal logging // @@ -245,28 +203,24 @@ def logColours(monochrome_logs=true) { return colorcodes } -// -// Attach the multiqc report to email -// -def attachMultiqcReport(multiqc_report) { - def mqc_report = null - try { - if (workflow.success) { - mqc_report = multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { - if (mqc_report.size() > 1) { - log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") - } - mqc_report = mqc_report[0] - } +// Return a single report from an object that may be a Path or List +// +def getSingleReport(multiqc_reports) { + if (multiqc_reports instanceof Path) { + return multiqc_reports + } else if (multiqc_reports instanceof List) { + if (multiqc_reports.size() == 0) { + log.warn("[${workflow.manifest.name}] No reports found from process 'MULTIQC'") + return null + } else if (multiqc_reports.size() == 1) { + return multiqc_reports.first() + } else { + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") + return multiqc_reports.first() } + } else { + return null } - catch (Exception all) { - if (multiqc_report) { - log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") - } - } - return mqc_report } // @@ -320,7 +274,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi email_fields['summary'] = summary << misc_fields // On success try attach the multiqc report - def mqc_report = attachMultiqcReport(multiqc_report) + def mqc_report = getSingleReport(multiqc_report) // Check if we are only sending emails on failure def email_address = email @@ -340,7 +294,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def email_html = html_template.toString() // Render the sendmail template - def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit + def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as MemoryUnit def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) @@ -351,14 +305,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi if (email_address) { try { if (plaintext_email) { -new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') + } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } ['sendmail', '-t'].execute() << sendmail_html log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") } - catch (Exception all) { + catch (Exception msg) { + log.debug(msg.toString()) + log.debug("Trying with mail instead of sendmail") // Catch failures and try with plaintext def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test index 1dc317f8..f117040c 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test @@ -41,26 +41,14 @@ nextflow_function { } } - test("Test Function workflowCitation") { - - function "workflowCitation" - - then { - assertAll( - { assert function.success }, - { assert snapshot(function.result).match() } - ) - } - } - - test("Test Function nfCoreLogo") { + test("Test Function without logColours") { - function "nfCoreLogo" + function "logColours" when { function { """ - input[0] = false + input[0] = true """ } } @@ -73,9 +61,8 @@ nextflow_function { } } - test("Test Function dashedLine") { - - function "dashedLine" + test("Test Function with logColours") { + function "logColours" when { function { @@ -93,14 +80,13 @@ nextflow_function { } } - test("Test Function without logColours") { - - function "logColours" + test("Test Function getSingleReport with a single file") { + function "getSingleReport" when { function { """ - input[0] = true + input[0] = file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true) """ } } @@ -108,18 +94,22 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") } ) } } - test("Test Function with logColours") { - function "logColours" + test("Test Function getSingleReport with multiple files") { + function "getSingleReport" when { function { """ - input[0] = false + input[0] = [ + file(params.modules_testdata_base_path + '/generic/tsv/test.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/network.tsv', checkIfExists: true), + file(params.modules_testdata_base_path + '/generic/tsv/expression.tsv', checkIfExists: true) + ] """ } } @@ -127,7 +117,9 @@ nextflow_function { then { assertAll( { assert function.success }, - { assert snapshot(function.result).match() } + { assert function.result.contains("test.tsv") }, + { assert !function.result.contains("network.tsv") }, + { assert !function.result.contains("expression.tsv") } ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap index 1037232c..02c67014 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap +++ b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap @@ -17,26 +17,6 @@ }, "timestamp": "2024-02-28T12:02:59.729647" }, - "Test Function nfCoreLogo": { - "content": [ - "\n\n-\u001b[2m----------------------------------------------------\u001b[0m-\n \u001b[0;32m,--.\u001b[0;30m/\u001b[0;32m,-.\u001b[0m\n\u001b[0;34m ___ __ __ __ ___ \u001b[0;32m/,-._.--~'\u001b[0m\n\u001b[0;34m |\\ | |__ __ / ` / \\ |__) |__ \u001b[0;33m} {\u001b[0m\n\u001b[0;34m | \\| | \\__, \\__/ | \\ |___ \u001b[0;32m\\`-._,-`-,\u001b[0m\n \u001b[0;32m`._,._,'\u001b[0m\n\u001b[0;35m nextflow_workflow v9.9.9\u001b[0m\n-\u001b[2m----------------------------------------------------\u001b[0m-\n" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:10.562934" - }, - "Test Function workflowCitation": { - "content": [ - "If you use nextflow_workflow for your analysis please cite:\n\n* The pipeline\n https://doi.org/10.5281/zenodo.5070524\n\n* The nf-core framework\n https://doi.org/10.1038/s41587-020-0439-x\n\n* Software dependencies\n https://github.com/nextflow_workflow/blob/master/CITATIONS.md" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:07.019761" - }, "Test Function without logColours": { "content": [ { @@ -95,16 +75,6 @@ }, "timestamp": "2024-02-28T12:03:17.969323" }, - "Test Function dashedLine": { - "content": [ - "-\u001b[2m----------------------------------------------------\u001b[0m-" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-02-28T12:03:14.366181" - }, "Test Function with logColours": { "content": [ { diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test index 842dc432..8fb30164 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -42,7 +42,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { @@ -94,7 +94,7 @@ nextflow_workflow { params { test_data = '' - outdir = 1 + outdir = null } workflow { diff --git a/tests/.nftignore b/tests/.nftignore index 7c0558cf..2b6598d3 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,21 +1,22 @@ -{bismark,bismark_hisat}/alignments/logs/*.txt -{bismark,bismark_hisat,bwameth}/{alignments,deduplicated}/*.{bam,bam.bai} -{bismark,bismark_hisat}/deduplicated/logs/*.txt -{bismark,bismark_hisat}/{reports,summary}/*.{html,txt} -bwameth/deduplicated/picard_metrics/*.txt +*/alignments/logs/*.txt +*/{alignments,deduplicated}/*.{bam,bam.bai} +*/deduplicated/logs/*.txt +*/{reports,summary}/*.{html,txt} +*/deduplicated/picard_metrics/*.txt fastqc/*.html fastqc/zips/*.zip -multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/*.{log,json} -multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_fastqc.txt -multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_general_stats.txt -multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt -multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_software_versions.txt -multiqc/{bismark,bismark_hisat,bwameth}/multiqc_data/multiqc_sources.txt -multiqc/{bismark,bismark_hisat,bwameth}/multiqc_report.html -multiqc/{bismark,bismark_hisat,bwameth}/multiqc_plots/{pdf,png,svg}/*.{pdf,png,svg} +multiqc/*/multiqc_data/*.{log,json} +multiqc/*/multiqc_data/multiqc_fastqc.txt +multiqc/*/multiqc_data/multiqc_general_stats.txt +multiqc/*/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt +multiqc/*/multiqc_data/multiqc_software_versions.txt +multiqc/*/multiqc_data/multiqc_sources.txt +multiqc/*/multiqc_report.html +multiqc/*/multiqc_plots/{pdf,png,svg}/*.{pdf,png,svg} pipeline_info/*.{html,json,txt,yml} -qualimap/**/qualimapReport.html -qualimap/**/css/* +*/qualimap/bamqc/*/qualimapReport.html +*/qualimap/bamqc/**/*.{pdf,png,svg} +*/qualimap/bamqc/*/css/* qualimap/**/images_qualimapReport/* qualimap/**/raw_data_qualimapReport/* trimgalore/fastqc/*.html diff --git a/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test b/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test new file mode 100644 index 00000000..24d63b1f --- /dev/null +++ b/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test @@ -0,0 +1,43 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + tag "cpu" + + test("Params: bismark | CAT_FASTQ | skip_trimming | skip_deduplication") { + when { + params { + input = "${projectDir}/assets/samplesheet_replicates.csv" + outdir = "$outputDir" + skip_trimming = true + skip_deduplication = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap b/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap new file mode 100644 index 00000000..fc01cbc3 --- /dev/null +++ b/tests/bismark_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap @@ -0,0 +1,263 @@ +{ + "Params: bismark | CAT_FASTQ | skip_trimming | skip_deduplication": { + "content": [ + 17, + { + "BISMARK_ALIGN": { + "bismark": "0.24.2" + }, + "BISMARK_GENOMEPREPARATION": { + "bismark": "0.24.2" + }, + "CAT_FASTQ": { + "cat": 9.5 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GUNZIP": { + "gunzip": 1.1 + }, + "Workflow": { + "nf-core/methylseq": "v3.0.0" + } + }, + [ + "bismark", + "bismark/alignments", + "bismark/alignments/Ecoli_10K_methylated.sorted.bam", + "bismark/alignments/Ecoli_10K_methylated.sorted.bam.bai", + "bismark/alignments/Ecoli_10K_methylated_R1_bismark_bt2_pe.bam", + "bismark/alignments/SRR389222.merged_bismark_bt2.bam", + "bismark/alignments/SRR389222.sorted.bam", + "bismark/alignments/SRR389222.sorted.bam.bai", + "bismark/alignments/logs", + "bismark/alignments/logs/Ecoli_10K_methylated_R1_bismark_bt2_PE_report.txt", + "bismark/alignments/logs/SRR389222.merged_bismark_bt2_SE_report.txt", + "bismark/deduplicated", + "bismark/methylation_calls", + "bismark/methylation_calls/bedGraph", + "bismark/methylation_calls/bedGraph/Ecoli_10K_methylated_R1_bismark_bt2_pe.bedGraph.gz", + "bismark/methylation_calls/bedGraph/SRR389222.merged_bismark_bt2.bedGraph.gz", + "bismark/methylation_calls/mbias", + "bismark/methylation_calls/mbias/Ecoli_10K_methylated_R1_bismark_bt2_pe.M-bias.txt", + "bismark/methylation_calls/mbias/SRR389222.merged_bismark_bt2.M-bias.txt", + "bismark/methylation_calls/methylation_calls", + "bismark/methylation_calls/methylation_calls/CHG_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz", + "bismark/methylation_calls/methylation_calls/CHG_OB_SRR389222.merged_bismark_bt2.txt.gz", + "bismark/methylation_calls/methylation_calls/CHG_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz", + "bismark/methylation_calls/methylation_calls/CHG_OT_SRR389222.merged_bismark_bt2.txt.gz", + "bismark/methylation_calls/methylation_calls/CHH_OB_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz", + "bismark/methylation_calls/methylation_calls/CHH_OB_SRR389222.merged_bismark_bt2.txt.gz", + "bismark/methylation_calls/methylation_calls/CHH_OT_Ecoli_10K_methylated_R1_bismark_bt2_pe.txt.gz", + "bismark/methylation_calls/methylation_calls/CHH_OT_SRR389222.merged_bismark_bt2.txt.gz", + 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"multiqc_citations.txt:md5,b205bd4d8278b41f2f712dfe7c740bce" + ], + [ + [ + "Ecoli_10K_methylated.sorted.bam", + "b49754b06cf7a7fc8d31b973e5ee9cc3" + ], + [ + "Ecoli_10K_methylated_R1_bismark_bt2_pe.bam", + "61d974d82ef679329077f6aac24de607" + ], + [ + "SRR389222.merged_bismark_bt2.bam", + "1d021c9012d2bac5b45e0f8b07d158ac" + ], + [ + "SRR389222.sorted.bam", + "7005f0e4ef98a2c93da133e9f59efcc7" + ] + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-12T03:52:20.737648964" + } +} diff --git a/tests/bismark_cytosine_report.nf.test b/tests/bismark_cytosine_report.nf.test new file mode 100644 index 00000000..7467c7bc --- /dev/null +++ b/tests/bismark_cytosine_report.nf.test @@ -0,0 +1,41 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + tag "cpu" + + test("Params: bismark | cytosine_report") { + when { + params { + cytosine_report = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bismark_cytosine_report.nf.test.snap b/tests/bismark_cytosine_report.nf.test.snap new file mode 100644 index 00000000..810644a4 --- /dev/null +++ b/tests/bismark_cytosine_report.nf.test.snap @@ -0,0 +1,386 @@ +{ + "Params: bismark | cytosine_report": { + "content": [ + 40, + { + "BISMARK_ALIGN": { + "bismark": "0.24.2" + }, + "BISMARK_GENOMEPREPARATION": { + "bismark": "0.24.2" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GUNZIP": { + "gunzip": 1.1 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.9, + "pigz": 2.8 + }, + "Workflow": { + "nf-core/methylseq": "v3.0.0" + } + }, + [ + "bismark", + "bismark/alignments", + "bismark/alignments/logs", + "bismark/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.txt", + "bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt", + "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", + 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"SRR389222_sub1.deduplicated.sorted.bam", + "3f11ef5fbbda3797fd6217728e4f00d3" + ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "b01f29fc1d8d46922a69df09c636b4c4" + ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "347195c04c9ffd2a2b10967a6682fc69" + ] + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-14T09:55:56.701520376" + } +} diff --git a/tests/bismark_emseq_clip_r1.nf.test b/tests/bismark_emseq_clip_r1.nf.test index c1bc57a0..aa268b82 100644 --- a/tests/bismark_emseq_clip_r1.nf.test +++ b/tests/bismark_emseq_clip_r1.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bismark | em_seq | clip_r1") { when { @@ -26,7 +27,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap index 2cff8aea..9a5aacac 100644 --- a/tests/bismark_emseq_clip_r1.nf.test.snap +++ b/tests/bismark_emseq_clip_r1.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | em_seq | clip_r1": { "content": [ - 43, + 36, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -12,15 +12,16 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ @@ -147,13 +148,8 @@ "multiqc/bismark/multiqc_data/multiqc_data.json", "multiqc/bismark/multiqc_data/multiqc_fastqc.txt", "multiqc/bismark/multiqc_data/multiqc_general_stats.txt", - "multiqc/bismark/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bismark/multiqc_data/multiqc_software_versions.txt", "multiqc/bismark/multiqc_data/multiqc_sources.txt", - "multiqc/bismark/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bismark/multiqc_data/qualimap_gc_content.txt", - "multiqc/bismark/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bismark/multiqc_data/qualimap_insert_size.txt", "multiqc/bismark/multiqc_plots", "multiqc/bismark/multiqc_plots/pdf", "multiqc/bismark/multiqc_plots/pdf/bismark-methylation-dp.pdf", @@ -186,10 +182,6 @@ "multiqc/bismark/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/bismark/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/bismark/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - 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"pipeline_info/nf_core_methylseq_software_mqc_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -540,16 +335,8 @@ "multiqc_bismark_alignment.txt:md5,4e1d3a0bc0619b11ac67ed685d5eb398", "multiqc_bismark_dedup.txt:md5,16e464f5bf2f1851a571ec87cbc1a0d9", "multiqc_bismark_methextract.txt:md5,ef3c68247a6254ae5e11e26052e3229e", - "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", - "qualimap_coverage_histogram.txt:md5,7d321d1eb204be4c3661364cf928c3e3", - "qualimap_gc_content.txt:md5,d914dc3ae413deb1db307910d9907ea9", - "qualimap_genome_fraction.txt:md5,2f6d7ae8cfdafc69358ce6a6800bef54", - "qualimap_insert_size.txt:md5,9a7301262b2927cc9587808fe1c7ff7f", - "genome_results.txt:md5,893c67bbc730a8af63e17cd7079c8701", - "genome_results.txt:md5,663f8e46c085b0b766479e809e461d65", - "genome_results.txt:md5,1d9640d93a711641a0554cf7f9d801f7", - "genome_results.txt:md5,3cafc0b75af4d9c78d41df9073a69332" + "multiqc_citations.txt:md5,73a6d29705d5a07f17f99c92e3a0f148", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ [ @@ -571,9 +358,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:26:16.42655233" + "timestamp": "2024-12-12T04:22:32.884719706" } -} \ No newline at end of file +} diff --git a/tests/bismark_hisat.nf.test b/tests/bismark_hisat.nf.test index 8ac37b1e..d78a7cfe 100644 --- a/tests/bismark_hisat.nf.test +++ b/tests/bismark_hisat.nf.test @@ -3,12 +3,13 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bismark_hisat") { when { params { - aligner = "bismark_hisat" - outdir = "$outputDir" + aligner = "bismark_hisat" + outdir = "$outputDir" } } @@ -25,7 +26,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bismark_hisat.nf.test.snap b/tests/bismark_hisat.nf.test.snap index 7672c433..16c77cd1 100644 --- a/tests/bismark_hisat.nf.test.snap +++ b/tests/bismark_hisat.nf.test.snap @@ -1,17 +1,17 @@ { "Params: bismark_hisat with hisat2-index": { "content": [ - 43 + 36 ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-12T07:21:45.007688275" + "timestamp": "2024-11-27T16:52:51.583828756" }, "Params: bismark_hisat": { "content": [ - 43, + 36, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -22,15 +22,16 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ @@ -157,13 +158,8 @@ "multiqc/bismark_hisat/multiqc_data/multiqc_data.json", "multiqc/bismark_hisat/multiqc_data/multiqc_fastqc.txt", "multiqc/bismark_hisat/multiqc_data/multiqc_general_stats.txt", - "multiqc/bismark_hisat/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bismark_hisat/multiqc_data/multiqc_software_versions.txt", "multiqc/bismark_hisat/multiqc_data/multiqc_sources.txt", - "multiqc/bismark_hisat/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bismark_hisat/multiqc_data/qualimap_gc_content.txt", - "multiqc/bismark_hisat/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bismark_hisat/multiqc_data/qualimap_insert_size.txt", "multiqc/bismark_hisat/multiqc_plots", "multiqc/bismark_hisat/multiqc_plots/pdf", "multiqc/bismark_hisat/multiqc_plots/pdf/bismark-methylation-dp.pdf", @@ -196,10 +192,6 @@ "multiqc/bismark_hisat/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/bismark_hisat/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/bismark_hisat/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/bismark_hisat/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bismark_hisat/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bismark_hisat/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bismark_hisat/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bismark_hisat/multiqc_plots/png", "multiqc/bismark_hisat/multiqc_plots/png/bismark-methylation-dp.png", "multiqc/bismark_hisat/multiqc_plots/png/bismark_alignment-cnt.png", @@ -231,10 +223,6 @@ "multiqc/bismark_hisat/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/bismark_hisat/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/bismark_hisat/multiqc_plots/png/general_stats_table.png", - "multiqc/bismark_hisat/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bismark_hisat/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bismark_hisat/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bismark_hisat/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bismark_hisat/multiqc_plots/svg", "multiqc/bismark_hisat/multiqc_plots/svg/bismark-methylation-dp.svg", "multiqc/bismark_hisat/multiqc_plots/svg/bismark_alignment-cnt.svg", @@ -266,204 +254,9 @@ "multiqc/bismark_hisat/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/bismark_hisat/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/bismark_hisat/multiqc_plots/svg/general_stats_table.svg", - "multiqc/bismark_hisat/multiqc_plots/svg/qualimap_coverage_histogram.svg", - 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"multiqc_bismark_methextract.txt:md5,5ce6739f6daa34276200f303c240e4b1", - "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", - "qualimap_coverage_histogram.txt:md5,b78964924f4985d97f6dff7ced688d29", - "qualimap_gc_content.txt:md5,ad345dd40fe367f2138776c8ea2b257f", - "qualimap_genome_fraction.txt:md5,9a1c3d3f7349cf1c2af1c5878dac4185", - "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd", - "genome_results.txt:md5,9b6cc47e6ecfa1a9bd03b79f9ab764e6", - "genome_results.txt:md5,e808a20446012ad2643385cf316605c0", - "genome_results.txt:md5,41833cb9a1cfb8945c0fd6711981e58e", - "genome_results.txt:md5,10636e2fb7eb1ac2cf246483405ae973" + "multiqc_citations.txt:md5,73a6d29705d5a07f17f99c92e3a0f148", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ [ @@ -583,9 +368,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:27:35.247058389" + "timestamp": "2024-12-12T04:24:31.364906851" } -} \ No newline at end of file +} diff --git a/tests/bismark_hisat_rrbs.nf.test b/tests/bismark_hisat_rrbs.nf.test index b8715634..665f45a8 100644 --- a/tests/bismark_hisat_rrbs.nf.test +++ b/tests/bismark_hisat_rrbs.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bismark_hisat | rrbs") { when { @@ -26,7 +27,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bismark_hisat_rrbs.nf.test.snap b/tests/bismark_hisat_rrbs.nf.test.snap index 7f48a90d..6a58914c 100644 --- a/tests/bismark_hisat_rrbs.nf.test.snap +++ b/tests/bismark_hisat_rrbs.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark_hisat | rrbs": { "content": [ - 39, + 32, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -12,15 +12,16 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ @@ -144,13 +145,8 @@ "multiqc/bismark_hisat/multiqc_data/multiqc_data.json", "multiqc/bismark_hisat/multiqc_data/multiqc_fastqc.txt", "multiqc/bismark_hisat/multiqc_data/multiqc_general_stats.txt", - "multiqc/bismark_hisat/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bismark_hisat/multiqc_data/multiqc_software_versions.txt", "multiqc/bismark_hisat/multiqc_data/multiqc_sources.txt", - "multiqc/bismark_hisat/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bismark_hisat/multiqc_data/qualimap_gc_content.txt", - "multiqc/bismark_hisat/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bismark_hisat/multiqc_data/qualimap_insert_size.txt", "multiqc/bismark_hisat/multiqc_plots", "multiqc/bismark_hisat/multiqc_plots/pdf", "multiqc/bismark_hisat/multiqc_plots/pdf/bismark-methylation-dp.pdf", @@ -181,10 +177,6 @@ "multiqc/bismark_hisat/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/bismark_hisat/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/bismark_hisat/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/bismark_hisat/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bismark_hisat/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bismark_hisat/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bismark_hisat/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bismark_hisat/multiqc_plots/png", "multiqc/bismark_hisat/multiqc_plots/png/bismark-methylation-dp.png", "multiqc/bismark_hisat/multiqc_plots/png/bismark_alignment-cnt.png", @@ -214,10 +206,6 @@ "multiqc/bismark_hisat/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/bismark_hisat/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/bismark_hisat/multiqc_plots/png/general_stats_table.png", - "multiqc/bismark_hisat/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bismark_hisat/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bismark_hisat/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bismark_hisat/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bismark_hisat/multiqc_plots/svg", "multiqc/bismark_hisat/multiqc_plots/svg/bismark-methylation-dp.svg", "multiqc/bismark_hisat/multiqc_plots/svg/bismark_alignment-cnt.svg", @@ -247,202 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"pipeline_info/nf_core_methylseq_software_mqc_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -529,16 +324,8 @@ "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", "multiqc_bismark_alignment.txt:md5,75a6ccfb5b5bff3a5b3d3e2174929fc3", "multiqc_bismark_methextract.txt:md5,d1312f03f47d7cc07ac18254cda720bd", - "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,8752cce2e7320f49516e897c60487831", - "qualimap_coverage_histogram.txt:md5,938111519a9ad1b2580f8f944fb659aa", - "qualimap_gc_content.txt:md5,3263a2edb88dcbddf5654df1b233f66d", - "qualimap_genome_fraction.txt:md5,5490f57857141d3e31a1f978bf1f7ead", - "qualimap_insert_size.txt:md5,65781ee04b024acd4efb4609a32d8b30", - "genome_results.txt:md5,371470c762818bb30e393e02eda189ef", - "genome_results.txt:md5,ef3cdabf2d57a1473996a8bae40c7c4e", - "genome_results.txt:md5,adb76fc6beedf9ed4fca89ff86f38285", - "genome_results.txt:md5,e6a04bc09af73e24da46fa1734a87300" + "multiqc_citations.txt:md5,73a6d29705d5a07f17f99c92e3a0f148", + "multiqc_cutadapt.txt:md5,8752cce2e7320f49516e897c60487831" ], [ [ @@ -576,9 +363,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:30:16.774897867" + "timestamp": "2024-12-12T04:28:32.797185084" } -} \ No newline at end of file +} diff --git a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test index 2f2b0a0c..5a34f073 100644 --- a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test +++ b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bismark_hisat | save_reference | save_align_intermeds") { when { @@ -27,7 +28,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap index ce353067..cf46b88c 100644 --- a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark_hisat | save_reference | save_align_intermeds": { "content": [ - 43, + 36, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -12,27 +12,28 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ "bismark_hisat", "bismark_hisat/alignments", - "bismark_hisat/alignments/Ecoli_10K_methylated.sorted.bam", + "bismark_hisat/alignments/Ecoli_10K_methylated.deduplicated.sorted.bam", "bismark_hisat/alignments/Ecoli_10K_methylated_1_val_1_bismark_hisat2_pe.bam", - "bismark_hisat/alignments/SRR389222_sub1.sorted.bam", + "bismark_hisat/alignments/SRR389222_sub1.deduplicated.sorted.bam", "bismark_hisat/alignments/SRR389222_sub1_trimmed_bismark_hisat2.bam", - "bismark_hisat/alignments/SRR389222_sub2.sorted.bam", + "bismark_hisat/alignments/SRR389222_sub2.deduplicated.sorted.bam", "bismark_hisat/alignments/SRR389222_sub2_trimmed_bismark_hisat2.bam", - "bismark_hisat/alignments/SRR389222_sub3.sorted.bam", + "bismark_hisat/alignments/SRR389222_sub3.deduplicated.sorted.bam", "bismark_hisat/alignments/SRR389222_sub3_trimmed_bismark_hisat2.bam", "bismark_hisat/alignments/logs", "bismark_hisat/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_hisat2_PE_report.txt", @@ -122,6 +123,7 @@ "bismark_hisat/reference_genome/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.7.ht2", "bismark_hisat/reference_genome/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.8.ht2", "bismark_hisat/reference_genome/BismarkIndex/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa", + "bismark_hisat/reference_genome/BismarkIndex/genome.fa", "bismark_hisat/reports", "bismark_hisat/reports/Ecoli_10K_methylated_1_val_1_bismark_hisat2_PE_report.html", "bismark_hisat/reports/SRR389222_sub1_trimmed_bismark_hisat2_SE_report.html", @@ -178,13 +180,8 @@ "multiqc/bismark_hisat/multiqc_data/multiqc_data.json", "multiqc/bismark_hisat/multiqc_data/multiqc_fastqc.txt", "multiqc/bismark_hisat/multiqc_data/multiqc_general_stats.txt", - "multiqc/bismark_hisat/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bismark_hisat/multiqc_data/multiqc_software_versions.txt", "multiqc/bismark_hisat/multiqc_data/multiqc_sources.txt", - "multiqc/bismark_hisat/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bismark_hisat/multiqc_data/qualimap_gc_content.txt", - "multiqc/bismark_hisat/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bismark_hisat/multiqc_data/qualimap_insert_size.txt", "multiqc/bismark_hisat/multiqc_plots", "multiqc/bismark_hisat/multiqc_plots/pdf", "multiqc/bismark_hisat/multiqc_plots/pdf/bismark-methylation-dp.pdf", @@ -217,10 +214,6 @@ "multiqc/bismark_hisat/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/bismark_hisat/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/bismark_hisat/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/bismark_hisat/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bismark_hisat/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bismark_hisat/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bismark_hisat/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bismark_hisat/multiqc_plots/png", "multiqc/bismark_hisat/multiqc_plots/png/bismark-methylation-dp.png", "multiqc/bismark_hisat/multiqc_plots/png/bismark_alignment-cnt.png", @@ -252,10 +245,6 @@ "multiqc/bismark_hisat/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/bismark_hisat/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/bismark_hisat/multiqc_plots/png/general_stats_table.png", - "multiqc/bismark_hisat/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bismark_hisat/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bismark_hisat/multiqc_plots/png/qualimap_genome_fraction.png", - 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"qualimap/SRR389222_sub3/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qualimap/SRR389222_sub3/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qualimap/SRR389222_sub3/raw_data_qualimapReport/mapping_quality_histogram.txt", + "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -564,6 +358,7 @@ "BS_GA.7.ht2:md5,9013eccd91ad614d7893c739275a394f", "BS_GA.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb", "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f", + "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,233409b9665cb851aca3b6b4511ff757", "bismark_alignment.txt:md5,3acfd1a751bef6696b6fa095d0631bb6", "bismark_deduplication.txt:md5,c025b4368b08f9e623624908632e44a1", @@ -591,20 +386,12 @@ "multiqc_bismark_alignment.txt:md5,731133921792ca3943acd7ae9938d5e7", "multiqc_bismark_dedup.txt:md5,5e58032548eda3c39384495cf0cfaa3d", "multiqc_bismark_methextract.txt:md5,5ce6739f6daa34276200f303c240e4b1", - "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", - "qualimap_coverage_histogram.txt:md5,b78964924f4985d97f6dff7ced688d29", - "qualimap_gc_content.txt:md5,ad345dd40fe367f2138776c8ea2b257f", - "qualimap_genome_fraction.txt:md5,9a1c3d3f7349cf1c2af1c5878dac4185", - "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd", - "genome_results.txt:md5,9b6cc47e6ecfa1a9bd03b79f9ab764e6", - "genome_results.txt:md5,e808a20446012ad2643385cf316605c0", - "genome_results.txt:md5,41833cb9a1cfb8945c0fd6711981e58e", - "genome_results.txt:md5,10636e2fb7eb1ac2cf246483405ae973" + "multiqc_citations.txt:md5,73a6d29705d5a07f17f99c92e3a0f148", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ [ - "Ecoli_10K_methylated.sorted.bam", + "Ecoli_10K_methylated.deduplicated.sorted.bam", "a1bd6455ebe3ecb43fe55e02d149d98" ], [ @@ -612,24 +399,24 @@ "534293d598c34366bcde057d3972b60" ], [ - "SRR389222_sub1.sorted.bam", - "b203a3936158c51706e56c3a4e16191e" + "SRR389222_sub1.deduplicated.sorted.bam", + "8d735d1f6337b2cf2fa720773ce34b60" ], [ "SRR389222_sub1_trimmed_bismark_hisat2.bam", "4ee84a71b73e58161226cc4d8ca1f9b9" ], [ - "SRR389222_sub2.sorted.bam", - "6f8b0d6f085cc6a3d597b8839ba94b8b" + "SRR389222_sub2.deduplicated.sorted.bam", + "45d53a598b4e59d173e32ea1f0558083" ], [ "SRR389222_sub2_trimmed_bismark_hisat2.bam", "3e3ccc351ed92abdced1edb24fbb94ed" ], [ - "SRR389222_sub3.sorted.bam", - "c03e8e797936ca18a7e286977c7cf16" + "SRR389222_sub3.deduplicated.sorted.bam", + "ddb15c5ef0686837616d73f45c154b8d" ], [ "SRR389222_sub3_trimmed_bismark_hisat2.bam", @@ -654,9 +441,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:31:35.562277469" + "timestamp": "2024-12-12T04:30:30.672354168" } -} \ No newline at end of file +} diff --git a/tests/bismark_nomeseq.nf.test b/tests/bismark_nomeseq.nf.test index 4cd98ef6..74a3ef2d 100644 --- a/tests/bismark_nomeseq.nf.test +++ b/tests/bismark_nomeseq.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bismark | nomeseq") { when { @@ -25,7 +26,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap index 1a0dfae7..bb7ed499 100644 --- a/tests/bismark_nomeseq.nf.test.snap +++ b/tests/bismark_nomeseq.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | nomeseq": { "content": [ - 47, + 40, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -12,15 +12,16 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ @@ -171,13 +172,8 @@ "multiqc/bismark/multiqc_data/multiqc_data.json", "multiqc/bismark/multiqc_data/multiqc_fastqc.txt", "multiqc/bismark/multiqc_data/multiqc_general_stats.txt", - "multiqc/bismark/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bismark/multiqc_data/multiqc_software_versions.txt", "multiqc/bismark/multiqc_data/multiqc_sources.txt", - "multiqc/bismark/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bismark/multiqc_data/qualimap_gc_content.txt", - "multiqc/bismark/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bismark/multiqc_data/qualimap_insert_size.txt", "multiqc/bismark/multiqc_plots", "multiqc/bismark/multiqc_plots/pdf", "multiqc/bismark/multiqc_plots/pdf/bismark-methylation-dp.pdf", @@ -210,10 +206,6 @@ "multiqc/bismark/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/bismark/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/bismark/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bismark/multiqc_plots/png", "multiqc/bismark/multiqc_plots/png/bismark-methylation-dp.png", "multiqc/bismark/multiqc_plots/png/bismark_alignment-cnt.png", @@ -245,10 +237,6 @@ "multiqc/bismark/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/bismark/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/bismark/multiqc_plots/png/general_stats_table.png", - "multiqc/bismark/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bismark/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bismark/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bismark/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bismark/multiqc_plots/svg", "multiqc/bismark/multiqc_plots/svg/bismark-methylation-dp.svg", "multiqc/bismark/multiqc_plots/svg/bismark_alignment-cnt.svg", @@ -280,204 +268,9 @@ "multiqc/bismark/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/bismark/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/bismark/multiqc_plots/svg/general_stats_table.svg", - 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"qualimap/SRR389222_sub3/raw_data_qualimapReport/coverage_across_reference.txt", - "qualimap/SRR389222_sub3/raw_data_qualimapReport/coverage_histogram.txt", - "qualimap/SRR389222_sub3/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qualimap/SRR389222_sub3/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qualimap/SRR389222_sub3/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qualimap/SRR389222_sub3/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qualimap/SRR389222_sub3/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qualimap/SRR389222_sub3/raw_data_qualimapReport/mapping_quality_histogram.txt", + "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -586,16 +379,8 @@ "multiqc_bismark_alignment.txt:md5,40ab86041f508d3f1a63bde20cab5440", "multiqc_bismark_dedup.txt:md5,d09a5de4d81a3207efb6a8937d060e46", "multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", - "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", - "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", - "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", - "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", - "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd", - "genome_results.txt:md5,e2a57140a56e0e4a1905c70084ccbb41", - "genome_results.txt:md5,69a3dc8568127c50b0decb29757230ee", - "genome_results.txt:md5,13d933d61649b837de72a418d5126c1b", - "genome_results.txt:md5,235830239cfc43d8e84c049b1e9b180a" + "multiqc_citations.txt:md5,73a6d29705d5a07f17f99c92e3a0f148", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ [ @@ -617,9 +402,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T16:37:19.615304198" + "timestamp": "2024-12-12T04:32:45.180359905" } -} \ No newline at end of file +} diff --git a/tests/bismark_rrbs.nf.test b/tests/bismark_rrbs.nf.test index 185a9998..971738c2 100644 --- a/tests/bismark_rrbs.nf.test +++ b/tests/bismark_rrbs.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bismark | rrbs") { when { @@ -25,7 +26,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap index 61dc63a1..5caa643b 100644 --- a/tests/bismark_rrbs.nf.test.snap +++ b/tests/bismark_rrbs.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | rrbs": { "content": [ - 39, + 32, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -12,15 +12,16 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ @@ -144,13 +145,8 @@ "multiqc/bismark/multiqc_data/multiqc_data.json", "multiqc/bismark/multiqc_data/multiqc_fastqc.txt", "multiqc/bismark/multiqc_data/multiqc_general_stats.txt", - "multiqc/bismark/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bismark/multiqc_data/multiqc_software_versions.txt", "multiqc/bismark/multiqc_data/multiqc_sources.txt", - "multiqc/bismark/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bismark/multiqc_data/qualimap_gc_content.txt", - "multiqc/bismark/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bismark/multiqc_data/qualimap_insert_size.txt", "multiqc/bismark/multiqc_plots", "multiqc/bismark/multiqc_plots/pdf", "multiqc/bismark/multiqc_plots/pdf/bismark-methylation-dp.pdf", @@ -181,10 +177,6 @@ "multiqc/bismark/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/bismark/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/bismark/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bismark/multiqc_plots/png", "multiqc/bismark/multiqc_plots/png/bismark-methylation-dp.png", "multiqc/bismark/multiqc_plots/png/bismark_alignment-cnt.png", @@ -214,10 +206,6 @@ "multiqc/bismark/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/bismark/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/bismark/multiqc_plots/png/general_stats_table.png", - "multiqc/bismark/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bismark/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bismark/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bismark/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bismark/multiqc_plots/svg", "multiqc/bismark/multiqc_plots/svg/bismark-methylation-dp.svg", "multiqc/bismark/multiqc_plots/svg/bismark_alignment-cnt.svg", @@ -247,202 +235,9 @@ "multiqc/bismark/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/bismark/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/bismark/multiqc_plots/svg/general_stats_table.svg", - "multiqc/bismark/multiqc_plots/svg/qualimap_coverage_histogram.svg", - 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"multiqc_bismark_methextract.txt:md5,1a2967a22fa1522f9e8d672fc43ca78d", - "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,8752cce2e7320f49516e897c60487831", - "qualimap_coverage_histogram.txt:md5,22c70e761489597e34a3d71d036ff190", - "qualimap_gc_content.txt:md5,c872803a08b92b36c136e2ba3bee96d4", - "qualimap_genome_fraction.txt:md5,393f86423cc89983ab66fa29f93dd710", - "qualimap_insert_size.txt:md5,65781ee04b024acd4efb4609a32d8b30", - "genome_results.txt:md5,678ca9b105799d1946f31a68d63927f5", - "genome_results.txt:md5,7a1ac1151afcc743a7a80ed68225346f", - "genome_results.txt:md5,eccab1342de8fbbf5e5e547cd861b704", - "genome_results.txt:md5,8b11703c6ee4e2a73d7d2624bda6b6ba" + "multiqc_citations.txt:md5,73a6d29705d5a07f17f99c92e3a0f148", + "multiqc_cutadapt.txt:md5,8752cce2e7320f49516e897c60487831" ], [ [ @@ -576,9 +363,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:34:25.708997835" + "timestamp": "2024-12-12T04:34:56.298752733" } -} \ No newline at end of file +} diff --git a/tests/bismark_run_preseq.nf.test b/tests/bismark_run_preseq.nf.test new file mode 100644 index 00000000..90a4f488 --- /dev/null +++ b/tests/bismark_run_preseq.nf.test @@ -0,0 +1,60 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + tag "cpu" + + test("Params: bismark | run_preseq") { + when { + params { + outdir = "$outputDir" + run_preseq = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Params: bismark | run_preseq with bowtie2-index") { + when { + params { + bismark_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz" + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size() + ).match() } + ) + } + } + +} diff --git a/tests/bismark_run_preseq.nf.test.snap b/tests/bismark_run_preseq.nf.test.snap new file mode 100644 index 00000000..ed543141 --- /dev/null +++ b/tests/bismark_run_preseq.nf.test.snap @@ -0,0 +1,376 @@ +{ + "Params: bismark | run_preseq": { + "content": [ + 36, + { + "BISMARK_ALIGN": { + "bismark": "0.24.2" + }, + "BISMARK_GENOMEPREPARATION": { + "bismark": "0.24.2" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GUNZIP": { + "gunzip": 1.1 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.9, + "pigz": 2.8 + }, + "Workflow": { + "nf-core/methylseq": "v3.0.0" + } + }, + [ + "bismark", + "bismark/alignments", + "bismark/alignments/logs", + "bismark/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.txt", + "bismark/alignments/logs/SRR389222_sub1_trimmed_bismark_bt2_SE_report.txt", + "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", + "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", + "bismark/deduplicated", + "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", + "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", + "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", + "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", + "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", + "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", + "bismark/deduplicated/logs", + "bismark/deduplicated/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplication_report.txt", + "bismark/deduplicated/logs/SRR389222_sub1_trimmed_bismark_bt2.deduplication_report.txt", + "bismark/deduplicated/logs/SRR389222_sub2_trimmed_bismark_bt2.deduplication_report.txt", + "bismark/deduplicated/logs/SRR389222_sub3_trimmed_bismark_bt2.deduplication_report.txt", + "bismark/methylation_calls", + "bismark/methylation_calls/bedGraph", + "bismark/methylation_calls/bedGraph/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.bedGraph.gz", + "bismark/methylation_calls/bedGraph/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "bismark/methylation_calls/bedGraph/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "bismark/methylation_calls/bedGraph/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.bedGraph.gz", + "bismark/methylation_calls/mbias", + "bismark/methylation_calls/mbias/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.deduplicated.M-bias.txt", + "bismark/methylation_calls/mbias/SRR389222_sub1_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "bismark/methylation_calls/mbias/SRR389222_sub2_trimmed_bismark_bt2.deduplicated.M-bias.txt", + "bismark/methylation_calls/mbias/SRR389222_sub3_trimmed_bismark_bt2.deduplicated.M-bias.txt", + 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index 00000000..5b8e9340 --- /dev/null +++ b/tests/bismark_run_qualimap.nf.test @@ -0,0 +1,41 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + tag "cpu" + + test("Params: bismark | run_qualimap") { + when { + params { + outdir = "$outputDir" + run_qualimap = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bismark_run_qualimap.nf.test.snap b/tests/bismark_run_qualimap.nf.test.snap new file mode 100644 index 00000000..e50cf433 --- /dev/null +++ b/tests/bismark_run_qualimap.nf.test.snap @@ -0,0 +1,623 @@ +{ + "Params: bismark | run_qualimap": { + "content": [ + 40, + { + "BISMARK_ALIGN": { + "bismark": "0.24.2" + }, + "BISMARK_GENOMEPREPARATION": { + "bismark": "0.24.2" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GUNZIP": { + "gunzip": 1.1 + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.9, + "pigz": 2.8 + }, + 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a/tests/bismark_save_reference_save_align_intermeds.nf.test b/tests/bismark_save_reference_save_align_intermeds.nf.test index cc5fc7a0..4d692362 100644 --- a/tests/bismark_save_reference_save_align_intermeds.nf.test +++ b/tests/bismark_save_reference_save_align_intermeds.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bismark | save_reference | save_align_intermeds") { when { @@ -27,7 +28,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap index 2f145429..c61a623f 100644 --- a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | save_reference | save_align_intermeds": { "content": [ - 43, + 36, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -12,27 +12,28 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ "bismark", "bismark/alignments", - "bismark/alignments/Ecoli_10K_methylated.sorted.bam", + "bismark/alignments/Ecoli_10K_methylated.deduplicated.sorted.bam", "bismark/alignments/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.bam", - "bismark/alignments/SRR389222_sub1.sorted.bam", + "bismark/alignments/SRR389222_sub1.deduplicated.sorted.bam", "bismark/alignments/SRR389222_sub1_trimmed_bismark_bt2.bam", - "bismark/alignments/SRR389222_sub2.sorted.bam", + "bismark/alignments/SRR389222_sub2.deduplicated.sorted.bam", "bismark/alignments/SRR389222_sub2_trimmed_bismark_bt2.bam", - "bismark/alignments/SRR389222_sub3.sorted.bam", + "bismark/alignments/SRR389222_sub3.deduplicated.sorted.bam", "bismark/alignments/SRR389222_sub3_trimmed_bismark_bt2.bam", "bismark/alignments/logs", "bismark/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.txt", @@ -118,6 +119,7 @@ "bismark/reference_genome/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.1.bt2", "bismark/reference_genome/BismarkIndex/Bisulfite_Genome/GA_conversion/BS_GA.rev.2.bt2", "bismark/reference_genome/BismarkIndex/Bisulfite_Genome/GA_conversion/genome_mfa.GA_conversion.fa", + "bismark/reference_genome/BismarkIndex/genome.fa", "bismark/reports", "bismark/reports/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.html", "bismark/reports/SRR389222_sub1_trimmed_bismark_bt2_SE_report.html", @@ -174,13 +176,8 @@ "multiqc/bismark/multiqc_data/multiqc_data.json", "multiqc/bismark/multiqc_data/multiqc_fastqc.txt", "multiqc/bismark/multiqc_data/multiqc_general_stats.txt", - "multiqc/bismark/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bismark/multiqc_data/multiqc_software_versions.txt", "multiqc/bismark/multiqc_data/multiqc_sources.txt", - "multiqc/bismark/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bismark/multiqc_data/qualimap_gc_content.txt", - "multiqc/bismark/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bismark/multiqc_data/qualimap_insert_size.txt", "multiqc/bismark/multiqc_plots", "multiqc/bismark/multiqc_plots/pdf", "multiqc/bismark/multiqc_plots/pdf/bismark-methylation-dp.pdf", @@ -213,10 +210,6 @@ "multiqc/bismark/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/bismark/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/bismark/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bismark/multiqc_plots/png", "multiqc/bismark/multiqc_plots/png/bismark-methylation-dp.png", "multiqc/bismark/multiqc_plots/png/bismark_alignment-cnt.png", @@ -248,10 +241,6 @@ "multiqc/bismark/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/bismark/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/bismark/multiqc_plots/png/general_stats_table.png", - "multiqc/bismark/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bismark/multiqc_plots/png/qualimap_gc_content.png", - 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"qualimap/SRR389222_sub3/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qualimap/SRR389222_sub3/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qualimap/SRR389222_sub3/raw_data_qualimapReport/mapping_quality_histogram.txt", + "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -556,6 +350,7 @@ "BS_GA.rev.1.bt2:md5,dabf2d6f80ba7e8fc96dfdc203f6bbfd", "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49", "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f", + "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de", "bismark-methylation-dp.txt:md5,dcbe642c42e31d8e480a2e46b97bbd45", "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b", "bismark_deduplication.txt:md5,db387240d46c09b0b952ed8b54855e76", @@ -583,20 +378,12 @@ "multiqc_bismark_alignment.txt:md5,40ab86041f508d3f1a63bde20cab5440", "multiqc_bismark_dedup.txt:md5,d09a5de4d81a3207efb6a8937d060e46", "multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", - "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", - "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", - "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", - "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", - "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd", - "genome_results.txt:md5,e2a57140a56e0e4a1905c70084ccbb41", - "genome_results.txt:md5,69a3dc8568127c50b0decb29757230ee", - "genome_results.txt:md5,13d933d61649b837de72a418d5126c1b", - "genome_results.txt:md5,235830239cfc43d8e84c049b1e9b180a" + "multiqc_citations.txt:md5,73a6d29705d5a07f17f99c92e3a0f148", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ [ - "Ecoli_10K_methylated.sorted.bam", + "Ecoli_10K_methylated.deduplicated.sorted.bam", "a54ab7c96f9523a4ccd25fd69f6905f8" ], [ @@ -604,24 +391,24 @@ "fad4414ebdaafdb15e0584b393400b27" ], [ - "SRR389222_sub1.sorted.bam", - "fa0f34c0d0d4d321b89973f23e033aa1" + "SRR389222_sub1.deduplicated.sorted.bam", + "3f11ef5fbbda3797fd6217728e4f00d3" ], [ "SRR389222_sub1_trimmed_bismark_bt2.bam", "934288bfc59d40ff7e73706d07815fb" ], [ - "SRR389222_sub2.sorted.bam", - "d347232a4fc5b1e02e98254b6ce97ae6" + "SRR389222_sub2.deduplicated.sorted.bam", + "b01f29fc1d8d46922a69df09c636b4c4" ], [ "SRR389222_sub2_trimmed_bismark_bt2.bam", "a94aeadc2acebd0a46647bb95acf2d55" ], [ - "SRR389222_sub3.sorted.bam", - "29648af285a183ae2194790b5a325186" + "SRR389222_sub3.deduplicated.sorted.bam", + "347195c04c9ffd2a2b10967a6682fc69" ], [ "SRR389222_sub3_trimmed_bismark_bt2.bam", @@ -646,9 +433,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:35:51.348052183" + "timestamp": "2024-12-12T04:42:48.283482818" } -} \ No newline at end of file +} diff --git a/tests/bismark_skip_deduplication.nf.test b/tests/bismark_skip_deduplication.nf.test index 055b77e6..8f91c23b 100644 --- a/tests/bismark_skip_deduplication.nf.test +++ b/tests/bismark_skip_deduplication.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bismark | skip_deduplication") { when { @@ -25,7 +26,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bismark_skip_deduplication.nf.test.snap b/tests/bismark_skip_deduplication.nf.test.snap index 6f4ff1ed..13e694bd 100644 --- a/tests/bismark_skip_deduplication.nf.test.snap +++ b/tests/bismark_skip_deduplication.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | skip_deduplication": { "content": [ - 39, + 32, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -12,23 +12,32 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ "bismark", "bismark/alignments", + "bismark/alignments/Ecoli_10K_methylated.sorted.bam", + "bismark/alignments/Ecoli_10K_methylated.sorted.bam.bai", "bismark/alignments/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.bam", + "bismark/alignments/SRR389222_sub1.sorted.bam", + "bismark/alignments/SRR389222_sub1.sorted.bam.bai", "bismark/alignments/SRR389222_sub1_trimmed_bismark_bt2.bam", + "bismark/alignments/SRR389222_sub2.sorted.bam", + "bismark/alignments/SRR389222_sub2.sorted.bam.bai", "bismark/alignments/SRR389222_sub2_trimmed_bismark_bt2.bam", + "bismark/alignments/SRR389222_sub3.sorted.bam", + "bismark/alignments/SRR389222_sub3.sorted.bam.bai", "bismark/alignments/SRR389222_sub3_trimmed_bismark_bt2.bam", "bismark/alignments/logs", "bismark/alignments/logs/Ecoli_10K_methylated_1_val_1_bismark_bt2_PE_report.txt", @@ -36,14 +45,6 @@ "bismark/alignments/logs/SRR389222_sub2_trimmed_bismark_bt2_SE_report.txt", "bismark/alignments/logs/SRR389222_sub3_trimmed_bismark_bt2_SE_report.txt", "bismark/deduplicated", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", - "bismark/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub1.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub2.deduplicated.sorted.bam.bai", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", - "bismark/deduplicated/SRR389222_sub3.deduplicated.sorted.bam.bai", "bismark/methylation_calls", "bismark/methylation_calls/bedGraph", "bismark/methylation_calls/bedGraph/Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.bedGraph.gz", @@ -144,13 +145,8 @@ "multiqc/bismark/multiqc_data/multiqc_data.json", "multiqc/bismark/multiqc_data/multiqc_fastqc.txt", "multiqc/bismark/multiqc_data/multiqc_general_stats.txt", - "multiqc/bismark/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bismark/multiqc_data/multiqc_software_versions.txt", "multiqc/bismark/multiqc_data/multiqc_sources.txt", - "multiqc/bismark/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bismark/multiqc_data/qualimap_gc_content.txt", - "multiqc/bismark/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bismark/multiqc_data/qualimap_insert_size.txt", "multiqc/bismark/multiqc_plots", "multiqc/bismark/multiqc_plots/pdf", "multiqc/bismark/multiqc_plots/pdf/bismark-methylation-dp.pdf", @@ -181,10 +177,6 @@ "multiqc/bismark/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/bismark/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/bismark/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bismark/multiqc_plots/png", "multiqc/bismark/multiqc_plots/png/bismark-methylation-dp.png", "multiqc/bismark/multiqc_plots/png/bismark_alignment-cnt.png", @@ -214,10 +206,6 @@ "multiqc/bismark/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/bismark/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/bismark/multiqc_plots/png/general_stats_table.png", - "multiqc/bismark/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bismark/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bismark/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bismark/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bismark/multiqc_plots/svg", "multiqc/bismark/multiqc_plots/svg/bismark-methylation-dp.svg", "multiqc/bismark/multiqc_plots/svg/bismark_alignment-cnt.svg", @@ -247,204 +235,9 @@ "multiqc/bismark/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/bismark/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/bismark/multiqc_plots/svg/general_stats_table.svg", - "multiqc/bismark/multiqc_plots/svg/qualimap_coverage_histogram.svg", - "multiqc/bismark/multiqc_plots/svg/qualimap_gc_content.svg", - 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"multiqc_bismark_methextract.txt:md5,374ad746b0cfa5143fc3606f77f53283", - "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", - "qualimap_coverage_histogram.txt:md5,dfd099755c43854826eb71acca153a33", - "qualimap_gc_content.txt:md5,55baed387d09b5a0583ce2b5abfc0d12", - "qualimap_genome_fraction.txt:md5,bde4b1a12ad8ad0420b44fa3f1ed0512", - "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd", - "genome_results.txt:md5,e2a57140a56e0e4a1905c70084ccbb41", - "genome_results.txt:md5,e26877c78ca30a559d5697938181c786", - "genome_results.txt:md5,7cfeccc601bb4a823e0ccf6bd32b4fb4", - "genome_results.txt:md5,2dd07533db9b09442aa391aea7b9a91f" + "multiqc_citations.txt:md5,73a6d29705d5a07f17f99c92e3a0f148", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ [ - "Ecoli_10K_methylated_1_val_1_bismark_bt2_pe.bam", - "fad4414ebdaafdb15e0584b393400b27" + "Ecoli_10K_methylated.sorted.bam", + 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"29648af285a183ae2194790b5a325186" ], [ - "SRR389222_sub3.deduplicated.sorted.bam", - "29648af285a183ae2194790b5a325186" + "SRR389222_sub3_trimmed_bismark_bt2.bam", + "6579ca7e49b9d7760ea5b3f3456739a1" ] ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:37:11.98959127" + "timestamp": "2024-12-12T04:44:49.927468765" } -} \ No newline at end of file +} diff --git a/tests/bismark_skip_multiqc.nf.test b/tests/bismark_skip_multiqc.nf.test index 99cbe91f..4f97d67c 100644 --- a/tests/bismark_skip_multiqc.nf.test +++ b/tests/bismark_skip_multiqc.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bismark | skip_multiqc") { when { @@ -25,7 +26,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bismark_skip_multiqc.nf.test.snap b/tests/bismark_skip_multiqc.nf.test.snap index 6f1e9301..9a099e70 100644 --- a/tests/bismark_skip_multiqc.nf.test.snap +++ b/tests/bismark_skip_multiqc.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | skip_multiqc": { "content": [ - 43, + 36, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -12,15 +12,16 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ @@ -147,13 +148,8 @@ "multiqc/bismark/multiqc_data/multiqc_data.json", "multiqc/bismark/multiqc_data/multiqc_fastqc.txt", "multiqc/bismark/multiqc_data/multiqc_general_stats.txt", - "multiqc/bismark/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bismark/multiqc_data/multiqc_software_versions.txt", "multiqc/bismark/multiqc_data/multiqc_sources.txt", - "multiqc/bismark/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bismark/multiqc_data/qualimap_gc_content.txt", - "multiqc/bismark/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bismark/multiqc_data/qualimap_insert_size.txt", "multiqc/bismark/multiqc_plots", "multiqc/bismark/multiqc_plots/pdf", "multiqc/bismark/multiqc_plots/pdf/bismark-methylation-dp.pdf", @@ -186,10 +182,6 @@ "multiqc/bismark/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/bismark/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/bismark/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bismark/multiqc_plots/png", "multiqc/bismark/multiqc_plots/png/bismark-methylation-dp.png", "multiqc/bismark/multiqc_plots/png/bismark_alignment-cnt.png", @@ -221,10 +213,6 @@ "multiqc/bismark/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/bismark/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/bismark/multiqc_plots/png/general_stats_table.png", - "multiqc/bismark/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bismark/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bismark/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bismark/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bismark/multiqc_plots/svg", 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"qualimap/SRR389222_sub3/raw_data_qualimapReport/mapping_quality_histogram.txt", + "pipeline_info/nf_core_methylseq_software_mqc_versions.yml", "trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -542,16 +335,8 @@ "multiqc_bismark_alignment.txt:md5,40ab86041f508d3f1a63bde20cab5440", "multiqc_bismark_dedup.txt:md5,d09a5de4d81a3207efb6a8937d060e46", "multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", - "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", - "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", - "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", - "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", - "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd", - "genome_results.txt:md5,e2a57140a56e0e4a1905c70084ccbb41", - "genome_results.txt:md5,69a3dc8568127c50b0decb29757230ee", - "genome_results.txt:md5,13d933d61649b837de72a418d5126c1b", - "genome_results.txt:md5,235830239cfc43d8e84c049b1e9b180a" + "multiqc_citations.txt:md5,73a6d29705d5a07f17f99c92e3a0f148", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ [ @@ -573,9 +358,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:38:34.022258124" + "timestamp": "2024-12-12T04:47:11.156071545" } -} \ No newline at end of file +} diff --git a/tests/bismark_skip_trimming.nf.test b/tests/bismark_skip_trimming.nf.test index 28b415c6..24d1bb11 100644 --- a/tests/bismark_skip_trimming.nf.test +++ b/tests/bismark_skip_trimming.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bismark | skip_trimming") { when { @@ -25,7 +26,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bismark_skip_trimming.nf.test.snap b/tests/bismark_skip_trimming.nf.test.snap index b0a9958c..46e38ad9 100644 --- a/tests/bismark_skip_trimming.nf.test.snap +++ b/tests/bismark_skip_trimming.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bismark | skip_trimming": { "content": [ - 39, + 32, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -12,11 +12,11 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ @@ -139,13 +139,8 @@ "multiqc/bismark/multiqc_data/multiqc_data.json", "multiqc/bismark/multiqc_data/multiqc_fastqc.txt", "multiqc/bismark/multiqc_data/multiqc_general_stats.txt", - "multiqc/bismark/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bismark/multiqc_data/multiqc_software_versions.txt", "multiqc/bismark/multiqc_data/multiqc_sources.txt", - "multiqc/bismark/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bismark/multiqc_data/qualimap_gc_content.txt", - "multiqc/bismark/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bismark/multiqc_data/qualimap_insert_size.txt", "multiqc/bismark/multiqc_plots", "multiqc/bismark/multiqc_plots/pdf", "multiqc/bismark/multiqc_plots/pdf/bismark-methylation-dp.pdf", @@ -174,10 +169,6 @@ "multiqc/bismark/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/bismark/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/bismark/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bismark/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bismark/multiqc_plots/png", "multiqc/bismark/multiqc_plots/png/bismark-methylation-dp.png", "multiqc/bismark/multiqc_plots/png/bismark_alignment-cnt.png", @@ -205,10 +196,6 @@ "multiqc/bismark/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/bismark/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/bismark/multiqc_plots/png/general_stats_table.png", - "multiqc/bismark/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bismark/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bismark/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bismark/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bismark/multiqc_plots/svg", 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"qualimap/SRR389222_sub3/raw_data_qualimapReport/mapping_quality_histogram.txt" + "pipeline_info/nf_core_methylseq_software_mqc_versions.yml" ], [ "Ecoli_10K_methylated_R1_bismark_bt2_pe.deduplicated.bedGraph.gz:md5,58c9ba98d0638c26a30233b006a81172", @@ -500,15 +292,7 @@ "multiqc_bismark_alignment.txt:md5,005c0d22d94af339b7145207dd64d92e", "multiqc_bismark_dedup.txt:md5,363c336840edee5ba1d2f40ce85aa2b6", "multiqc_bismark_methextract.txt:md5,8c74286850870be34285f1b8a96ab641", - "multiqc_citations.txt:md5,3a8f645306d124626931e2eb6ade3dfc", - "qualimap_coverage_histogram.txt:md5,937adee56f45d795a2dc79d4eeb6704d", - "qualimap_gc_content.txt:md5,d1c2209fd60ab1ef987dcdcbf11ace26", - "qualimap_genome_fraction.txt:md5,e9d696b5fb6e7a660e69b378039907a5", - "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd", - "genome_results.txt:md5,024419d0c463732287b0edf27647e21a", - "genome_results.txt:md5,445e1cd701e53837e7747383264f0b15", - "genome_results.txt:md5,cb7e3c8a8097ffd58fc9d4b0f293cf64", - "genome_results.txt:md5,56b2c5bc4772ef6439af3a3b8c97cfaa" + "multiqc_citations.txt:md5,b205bd4d8278b41f2f712dfe7c740bce" ], [ [ @@ -530,9 +314,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-17T11:09:41.623493366" + "timestamp": "2024-11-28T09:55:44.514046309" } } diff --git a/tests/bwameth.nf.test b/tests/bwameth.nf.test index 04283574..281f49b2 100644 --- a/tests/bwameth.nf.test +++ b/tests/bwameth.nf.test @@ -3,12 +3,13 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bwameth") { when { params { - aligner = "bwameth" - outdir = "$outputDir" + aligner = "bwameth" + outdir = "$outputDir" } } @@ -18,14 +19,14 @@ nextflow_pipeline { // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') // bam_files: All bam files - def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) assertAll( { assert workflow.success}, { assert snapshot( // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents @@ -40,9 +41,9 @@ nextflow_pipeline { test("Params: bwameth with bwameth-index") { when { params { - aligner = "bwameth" + aligner = "bwameth" bwameth_index = "https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bwameth_Index.tar.gz" - outdir = "$outputDir" + outdir = "$outputDir" } } diff --git a/tests/bwameth.nf.test.snap b/tests/bwameth.nf.test.snap index 5d804e01..9b16a241 100644 --- a/tests/bwameth.nf.test.snap +++ b/tests/bwameth.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bwameth": { "content": [ - 50, + 47, { "BWAMETH_ALIGN": { "bwameth": "0.2.7" @@ -12,15 +12,16 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ @@ -36,12 +37,16 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", + "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -95,7 +100,6 @@ "multiqc/bwameth/multiqc_data/multiqc_fastqc.txt", "multiqc/bwameth/multiqc_data/multiqc_general_stats.txt", "multiqc/bwameth/multiqc_data/multiqc_picard_dups.txt", - "multiqc/bwameth/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bwameth/multiqc_data/multiqc_samtools_flagstat.txt", "multiqc/bwameth/multiqc_data/multiqc_samtools_stats.txt", "multiqc/bwameth/multiqc_data/multiqc_software_versions.txt", @@ -104,10 +108,6 @@ "multiqc/bwameth/multiqc_data/picard_histogram.txt", "multiqc/bwameth/multiqc_data/picard_histogram_1.txt", "multiqc/bwameth/multiqc_data/picard_histogram_2.txt", - "multiqc/bwameth/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bwameth/multiqc_data/qualimap_gc_content.txt", - "multiqc/bwameth/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bwameth/multiqc_data/qualimap_insert_size.txt", "multiqc/bwameth/multiqc_data/samtools-flagstat-dp_Percentage_of_total.txt", "multiqc/bwameth/multiqc_data/samtools-flagstat-dp_Read_counts.txt", "multiqc/bwameth/multiqc_data/samtools-stats-dp.txt", @@ -133,10 +133,6 @@ "multiqc/bwameth/multiqc_plots/pdf/general_stats_table.pdf", "multiqc/bwameth/multiqc_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/bwameth/multiqc_plots/pdf/picard_deduplication-pct.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-stats-dp.pdf", @@ -162,10 +158,6 @@ "multiqc/bwameth/multiqc_plots/png/general_stats_table.png", "multiqc/bwameth/multiqc_plots/png/picard_deduplication-cnt.png", "multiqc/bwameth/multiqc_plots/png/picard_deduplication-pct.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bwameth/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/bwameth/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/bwameth/multiqc_plots/png/samtools-stats-dp.png", @@ -191,10 +183,6 @@ "multiqc/bwameth/multiqc_plots/svg/general_stats_table.svg", "multiqc/bwameth/multiqc_plots/svg/picard_deduplication-cnt.svg", "multiqc/bwameth/multiqc_plots/svg/picard_deduplication-pct.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_coverage_histogram.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_gc_content.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_genome_fraction.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_insert_size.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-stats-dp.svg", @@ -202,146 +190,7 @@ "multiqc/bwameth/multiqc_plots/svg/samtools_alignment_plot-pct.svg", "multiqc/bwameth/multiqc_report.html", "pipeline_info", - 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"qualimap/Ecoli_10K_methylated/raw_data_qualimapReport/coverage_histogram.txt", - "qualimap/Ecoli_10K_methylated/raw_data_qualimapReport/duplication_rate_histogram.txt", - "qualimap/Ecoli_10K_methylated/raw_data_qualimapReport/genome_fraction_coverage.txt", - "qualimap/Ecoli_10K_methylated/raw_data_qualimapReport/homopolymer_indels.txt", - "qualimap/Ecoli_10K_methylated/raw_data_qualimapReport/insert_size_across_reference.txt", - "qualimap/Ecoli_10K_methylated/raw_data_qualimapReport/insert_size_histogram.txt", - "qualimap/Ecoli_10K_methylated/raw_data_qualimapReport/mapped_reads_clipping_profile.txt", - "qualimap/Ecoli_10K_methylated/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt", - "qualimap/Ecoli_10K_methylated/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt", - "qualimap/Ecoli_10K_methylated/raw_data_qualimapReport/mapping_quality_across_reference.txt", - "qualimap/Ecoli_10K_methylated/raw_data_qualimapReport/mapping_quality_histogram.txt", - "qualimap/SRR389222_sub1", - "qualimap/SRR389222_sub1/css", - "qualimap/SRR389222_sub1/css/agogo.css", - "qualimap/SRR389222_sub1/css/ajax-loader.gif", - "qualimap/SRR389222_sub1/css/basic.css", - "qualimap/SRR389222_sub1/css/bgfooter.png", - "qualimap/SRR389222_sub1/css/bgtop.png", - "qualimap/SRR389222_sub1/css/comment-bright.png", - "qualimap/SRR389222_sub1/css/comment-close.png", - "qualimap/SRR389222_sub1/css/comment.png", - "qualimap/SRR389222_sub1/css/doctools.js", - "qualimap/SRR389222_sub1/css/down-pressed.png", - "qualimap/SRR389222_sub1/css/down.png", - "qualimap/SRR389222_sub1/css/file.png", - "qualimap/SRR389222_sub1/css/jquery.js", - "qualimap/SRR389222_sub1/css/minus.png", - "qualimap/SRR389222_sub1/css/plus.png", - "qualimap/SRR389222_sub1/css/pygments.css", - "qualimap/SRR389222_sub1/css/qualimap_logo_small.png", - "qualimap/SRR389222_sub1/css/report.css", - "qualimap/SRR389222_sub1/css/searchtools.js", - "qualimap/SRR389222_sub1/css/underscore.js", - 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-364,13 +213,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,2df1b94e099f2948ad990224f7cf07a4", + "Ecoli_10K_methylated.stats:md5,be3e2bea0d6867aab35d06bfbdae0aa2", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,0f660ccc767662d4bd8c5197f3d46a87", + "SRR389222_sub1.stats:md5,21e116cc6374c4a2d55d2c383cd4281e", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,9343b74f4d825bfb2a554be3d8bed432", + "SRR389222_sub2.stats:md5,75cb0f1e953843150e3b217ec3f271da", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,f41e135f71893e2a8b589c4a66cbfeec", + "SRR389222_sub3.stats:md5,6876e424094ecdf302bd2097f8e21b1c", "Ecoli_10K_methylated.markdup.sorted_CpG.bedGraph:md5,d3bce01078b6e7749f3906bf9faad5b5", "SRR389222_sub1.markdup.sorted_CpG.bedGraph:md5,0944ad0e3b05791bf6dfd06be7ca4af1", "SRR389222_sub2.markdup.sorted_CpG.bedGraph:md5,0a3c19af55d1625e91903ae25d1d2098", @@ -393,41 +242,49 @@ "fastqc_sequence_counts_plot.txt:md5,58eeeb06bc9dcc1764c7daf0847d6bbf", "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", - "multiqc_citations.txt:md5,581df5b266851d0244e7cfb213351ffb", + "multiqc_citations.txt:md5,ad6c1e326b4276501a3b42eaad747de1", "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "multiqc_picard_dups.txt:md5,82eaab96189f22fd93db38bb516ba6a5", "multiqc_samtools_flagstat.txt:md5,a8f5b45b8b3412a9adc3dd0d35208c73", - "multiqc_samtools_stats.txt:md5,e24271a8111b06c1f545b6b1a077a4a7", + "multiqc_samtools_stats.txt:md5,bfcab6a9bd26872ecd2ec469d222c70b", "picard_deduplication.txt:md5,7dacf4d4e0d7d2d9a7205beecfa7125c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "qualimap_coverage_histogram.txt:md5,c7c932e4d84b735bd434c1aaa713b6e6", - "qualimap_gc_content.txt:md5,893d1acba7a6675ff9e2eff2985fa4e3", - "qualimap_genome_fraction.txt:md5,ef5b6010b52a03f6e58356db7128d0dc", - "qualimap_insert_size.txt:md5,f86cc9fe7a12af8f62f26312660e9225", "samtools-flagstat-dp_Percentage_of_total.txt:md5,ff5d65a480449ba98587c43f3a2bd33e", "samtools-flagstat-dp_Read_counts.txt:md5,6a5332e2ad59f7da00b5a9a1a25fd2f8", "samtools-stats-dp.txt:md5,52021b9a9455b39b39dd357bc2e8d346", - "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b", - "genome_results.txt:md5,1ee2e29ac41c2cd7e6a0f00741e8d16e", - "genome_results.txt:md5,2c755b15ae5ad4a1d29395320a6264ca", - "genome_results.txt:md5,2294badeccd2e8870fd6c60d115687b0", - "genome_results.txt:md5,4da1144933d094185d02f7482c120804" + "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b" ], [ + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "a2921f761f431ede522016f83f75c12d" + ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "e50275d6d44138f19d65ee479444d5ce" + ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "d365b8b2662b2abffb51dd67a1f463b4" + ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "a9fd2900b9d759f8f4f62cbbb2744fde" + ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -435,19 +292,19 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:41:20.919214758" + "timestamp": "2024-12-12T04:51:56.426651348" }, "Params: bwameth with bwameth-index": { "content": [ - 50 + 47 ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-12T07:40:41.336750081" + "timestamp": "2024-11-27T17:25:00.644734614" } -} \ No newline at end of file +} diff --git a/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test b/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test new file mode 100644 index 00000000..07d797ea --- /dev/null +++ b/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test @@ -0,0 +1,44 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + tag "cpu" + + test("Params: bwameth | CAT_FASTQ | skip_trimming | skip_deduplication") { + when { + params { + input = "${projectDir}/assets/samplesheet_replicates.csv" + aligner = "bwameth" + outdir = "$outputDir" + skip_trimming = true + skip_deduplication = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap b/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap new file mode 100644 index 00000000..c4994328 --- /dev/null +++ b/tests/bwameth_cat_fastq_skip_trimming_skip_deduplication.nf.test.snap @@ -0,0 +1,187 @@ +{ + "Params: bwameth | CAT_FASTQ | skip_trimming | skip_deduplication": { + "content": [ + 20, + { + "BWAMETH_ALIGN": { + "bwameth": "0.2.7" + }, + "BWAMETH_INDEX": { + "bwameth": "0.2.7" + }, + "CAT_FASTQ": { + "cat": 9.5 + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GUNZIP": { + "gunzip": 1.1 + }, + "Workflow": { + "nf-core/methylseq": "v3.0.0" + } + }, + [ + "bwameth", + "bwameth/alignments", + "bwameth/alignments/Ecoli_10K_methylated.sorted.bam", + "bwameth/alignments/SRR389222.sorted.bam", + "bwameth/alignments/samtools_stats", + "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.flagstat", + "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.stats", + "bwameth/alignments/samtools_stats/SRR389222.flagstat", + "bwameth/alignments/samtools_stats/SRR389222.stats", + "bwameth/deduplicated", + "cat", + "cat/SRR389222.merged.fastq.gz", + "fastqc", + "fastqc/Ecoli_10K_methylated_1_fastqc.html", + "fastqc/Ecoli_10K_methylated_2_fastqc.html", + "fastqc/SRR389222_fastqc.html", + "fastqc/zips", + "fastqc/zips/Ecoli_10K_methylated_1_fastqc.zip", + "fastqc/zips/Ecoli_10K_methylated_2_fastqc.zip", + "fastqc/zips/SRR389222_fastqc.zip", + "methyldackel", + "methyldackel/Ecoli_10K_methylated.sorted_CpG.bedGraph", + "methyldackel/SRR389222.sorted_CpG.bedGraph", + "methyldackel/mbias", + "methyldackel/mbias/Ecoli_10K_methylated.mbias.txt", + "methyldackel/mbias/SRR389222.mbias.txt", + "multiqc", + "multiqc/bwameth", + "multiqc/bwameth/multiqc_data", + "multiqc/bwameth/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/bwameth/multiqc_data/fastqc_adapter_content_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/bwameth/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/bwameth/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_sequence_counts_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/bwameth/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/bwameth/multiqc_data/multiqc.log", + "multiqc/bwameth/multiqc_data/multiqc_citations.txt", + "multiqc/bwameth/multiqc_data/multiqc_data.json", + "multiqc/bwameth/multiqc_data/multiqc_fastqc.txt", + "multiqc/bwameth/multiqc_data/multiqc_general_stats.txt", + "multiqc/bwameth/multiqc_data/multiqc_samtools_flagstat.txt", + "multiqc/bwameth/multiqc_data/multiqc_samtools_stats.txt", + "multiqc/bwameth/multiqc_data/multiqc_software_versions.txt", + "multiqc/bwameth/multiqc_data/multiqc_sources.txt", + "multiqc/bwameth/multiqc_data/samtools-flagstat-dp_Percentage_of_total.txt", + "multiqc/bwameth/multiqc_data/samtools-flagstat-dp_Read_counts.txt", + "multiqc/bwameth/multiqc_data/samtools-stats-dp.txt", + "multiqc/bwameth/multiqc_data/samtools_alignment_plot.txt", + "multiqc/bwameth/multiqc_plots", + "multiqc/bwameth/multiqc_plots/pdf", + "multiqc/bwameth/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/bwameth/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf", + "multiqc/bwameth/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", + "multiqc/bwameth/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/bwameth/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/bwameth/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/bwameth/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/bwameth/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/bwameth/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/bwameth/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/bwameth/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/bwameth/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/bwameth/multiqc_plots/pdf/general_stats_table.pdf", + "multiqc/bwameth/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", + "multiqc/bwameth/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", + "multiqc/bwameth/multiqc_plots/pdf/samtools-stats-dp.pdf", + "multiqc/bwameth/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf", + "multiqc/bwameth/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", + "multiqc/bwameth/multiqc_plots/png", + "multiqc/bwameth/multiqc_plots/png/fastqc-status-check-heatmap.png", + "multiqc/bwameth/multiqc_plots/png/fastqc_adapter_content_plot.png", + "multiqc/bwameth/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png", + "multiqc/bwameth/multiqc_plots/png/fastqc_per_base_n_content_plot.png", + "multiqc/bwameth/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", + "multiqc/bwameth/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", + "multiqc/bwameth/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", + "multiqc/bwameth/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", + "multiqc/bwameth/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", + "multiqc/bwameth/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", + "multiqc/bwameth/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/bwameth/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/bwameth/multiqc_plots/png/general_stats_table.png", + "multiqc/bwameth/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png", + "multiqc/bwameth/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png", + "multiqc/bwameth/multiqc_plots/png/samtools-stats-dp.png", + "multiqc/bwameth/multiqc_plots/png/samtools_alignment_plot-cnt.png", + "multiqc/bwameth/multiqc_plots/png/samtools_alignment_plot-pct.png", + "multiqc/bwameth/multiqc_plots/svg", + "multiqc/bwameth/multiqc_plots/svg/fastqc-status-check-heatmap.svg", + "multiqc/bwameth/multiqc_plots/svg/fastqc_adapter_content_plot.svg", + "multiqc/bwameth/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", + "multiqc/bwameth/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", + "multiqc/bwameth/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", + "multiqc/bwameth/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", + "multiqc/bwameth/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/bwameth/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", + "multiqc/bwameth/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", + "multiqc/bwameth/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", + "multiqc/bwameth/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/bwameth/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/bwameth/multiqc_plots/svg/general_stats_table.svg", + "multiqc/bwameth/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", + "multiqc/bwameth/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg", + "multiqc/bwameth/multiqc_plots/svg/samtools-stats-dp.svg", + "multiqc/bwameth/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", + "multiqc/bwameth/multiqc_plots/svg/samtools_alignment_plot-pct.svg", + "multiqc/bwameth/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_methylseq_software_mqc_versions.yml" + ], + [ + "Ecoli_10K_methylated.flagstat:md5,7c3bae0f9c700dde88785a7e94c6ae2c", + "Ecoli_10K_methylated.stats:md5,9edddeee18b48d32e6f0784180af3655", + "SRR389222.flagstat:md5,a90f1bdcb30f4d0597ccf69fe0b37b1f", + "SRR389222.stats:md5,ff112795ace81e3e93cd3e4b42466a7a", + "SRR389222.merged.fastq.gz:md5,47e1d7461d511a970e80085dd6454775", + "Ecoli_10K_methylated.sorted_CpG.bedGraph:md5,3656c54896013b76de978ab95c3f5975", + "SRR389222.sorted_CpG.bedGraph:md5,a754358e8b95db30602aa29835a896bd", + "Ecoli_10K_methylated.mbias.txt:md5,ec13da6deba1ce147624bce065ec5df6", + "SRR389222.mbias.txt:md5,fce04d733e066d0b933cedc602e2af81", + "fastqc-status-check-heatmap.txt:md5,04ba1bfaa7df8fb71d5a058e2463029f", + "fastqc_adapter_content_plot.txt:md5,48d8bd5ece984a74972ce0a0e814dd07", + "fastqc_overrepresented_sequences_plot.txt:md5,a94413e4d294e8161658bb5593387edb", + "fastqc_per_base_n_content_plot.txt:md5,35a2ea915454dffa9c49c9de3c64d9e2", + "fastqc_per_base_sequence_quality_plot.txt:md5,62d571e9630a013069ceaf04e57575c8", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,f6875166fc8698a3c9be67ee4a6c901b", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f1728b050adcecaea15150839d588147", + "fastqc_per_sequence_quality_scores_plot.txt:md5,f561d95db7dcaf6bf694e319cf45b98d", + "fastqc_sequence_counts_plot.txt:md5,33099ff26b32a6906c63c4cc1f113b33", + "fastqc_sequence_duplication_levels_plot.txt:md5,3c08938b1fd0e2add3d43ab80e77e234", + "fastqc_top_overrepresented_sequences_table.txt:md5,773be2a83a2e566f1b1820e45071bb02", + "multiqc_citations.txt:md5,ee1baba4adea57b43a9ae59ce7e1dd7f", + "multiqc_samtools_flagstat.txt:md5,1b1334c82b33c933faffd61e41ab5a89", + "multiqc_samtools_stats.txt:md5,40b4c6c853ab4089fbb894be13085a1e", + "samtools-flagstat-dp_Percentage_of_total.txt:md5,87680f6ccb06edba6b75236eed4a7320", + "samtools-flagstat-dp_Read_counts.txt:md5,f757c55b3b0dedfbde58086dd09cd2f2", + "samtools-stats-dp.txt:md5,0e448f198b0ad0efd2b19fb55c48daa1", + "samtools_alignment_plot.txt:md5,e2c576d011f363417fb894279d43d5b9" + ], + [ + [ + "Ecoli_10K_methylated.sorted.bam", + "5b485bcabdb1ad5955cfa061741fad31" + ], + [ + "SRR389222.sorted.bam", + "58e56b24ab2e33a41b7753fbe9c2b1e6" + ] + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.2" + }, + "timestamp": "2024-12-12T03:55:34.354490971" + } +} diff --git a/tests/bwameth_rrbs.nf.test b/tests/bwameth_rrbs.nf.test index cc0fba43..f3a6b0fc 100644 --- a/tests/bwameth_rrbs.nf.test +++ b/tests/bwameth_rrbs.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bwameth | rrbs") { when { @@ -26,7 +27,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bwameth_rrbs.nf.test.snap b/tests/bwameth_rrbs.nf.test.snap index f2c5c583..1bf48be2 100644 --- a/tests/bwameth_rrbs.nf.test.snap +++ b/tests/bwameth_rrbs.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bwameth | rrbs": { "content": [ - 42, + 39, { "BWAMETH_ALIGN": { "bwameth": "0.2.7" @@ -12,15 +12,16 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ @@ -35,6 +36,11 @@ "bwameth/alignments/samtools_stats/SRR389222_sub2.stats", "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", + "bwameth/deduplicated", + "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", + "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", + "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", + "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "fastqc", "fastqc/Ecoli_10K_methylated_1_fastqc.html", "fastqc/Ecoli_10K_methylated_2_fastqc.html", @@ -48,10 +54,10 @@ "fastqc/zips/SRR389222_sub2_fastqc.zip", "fastqc/zips/SRR389222_sub3_fastqc.zip", "methyldackel", - "methyldackel/Ecoli_10K_methylated.sorted_CpG.bedGraph", - "methyldackel/SRR389222_sub1.sorted_CpG.bedGraph", - "methyldackel/SRR389222_sub2.sorted_CpG.bedGraph", - "methyldackel/SRR389222_sub3.sorted_CpG.bedGraph", + "methyldackel/Ecoli_10K_methylated.deduplicated.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub1.deduplicated.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub2.deduplicated.sorted_CpG.bedGraph", + "methyldackel/SRR389222_sub3.deduplicated.sorted_CpG.bedGraph", "methyldackel/mbias", "methyldackel/mbias/Ecoli_10K_methylated.mbias.txt", "methyldackel/mbias/SRR389222_sub1.mbias.txt", @@ -80,15 +86,10 @@ "multiqc/bwameth/multiqc_data/multiqc_data.json", "multiqc/bwameth/multiqc_data/multiqc_fastqc.txt", "multiqc/bwameth/multiqc_data/multiqc_general_stats.txt", - "multiqc/bwameth/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bwameth/multiqc_data/multiqc_samtools_flagstat.txt", "multiqc/bwameth/multiqc_data/multiqc_samtools_stats.txt", "multiqc/bwameth/multiqc_data/multiqc_software_versions.txt", "multiqc/bwameth/multiqc_data/multiqc_sources.txt", - "multiqc/bwameth/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bwameth/multiqc_data/qualimap_gc_content.txt", - "multiqc/bwameth/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bwameth/multiqc_data/qualimap_insert_size.txt", "multiqc/bwameth/multiqc_data/samtools-flagstat-dp_Percentage_of_total.txt", "multiqc/bwameth/multiqc_data/samtools-flagstat-dp_Read_counts.txt", "multiqc/bwameth/multiqc_data/samtools-stats-dp.txt", @@ -112,10 +113,6 @@ "multiqc/bwameth/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/bwameth/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/bwameth/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-stats-dp.pdf", @@ -139,10 +136,6 @@ "multiqc/bwameth/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/bwameth/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/bwameth/multiqc_plots/png/general_stats_table.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bwameth/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/bwameth/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/bwameth/multiqc_plots/png/samtools-stats-dp.png", @@ -166,10 +159,6 @@ "multiqc/bwameth/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/bwameth/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/bwameth/multiqc_plots/svg/general_stats_table.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_coverage_histogram.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_gc_content.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_genome_fraction.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_insert_size.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-stats-dp.svg", @@ -177,146 +166,7 @@ "multiqc/bwameth/multiqc_plots/svg/samtools_alignment_plot-pct.svg", "multiqc/bwameth/multiqc_report.html", "pipeline_info", - "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", - "qualimap", - "qualimap/Ecoli_10K_methylated", - "qualimap/Ecoli_10K_methylated/css", - "qualimap/Ecoli_10K_methylated/css/agogo.css", - 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"genome_results.txt:md5,1466a5585ad5887f8fea7af2732efcba", - "genome_results.txt:md5,58d212848ac7b7650e3bd6812a4064af" + "samtools_alignment_plot.txt:md5,e10b792693e5a69776f623f5f7de647e" ], [ - + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "8039fd2db60f8ca71daa444e62411f53" + ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "a75ccc7cde779aac54662b03e5c01fe0" + ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "82d2a7df2d4cb1ed2ea1e0456aff1cb" + ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "7856b5549c566fb795c46f0674e069e1" + ] ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:43:36.391049268" + "timestamp": "2024-12-12T04:55:27.178782157" } -} \ No newline at end of file +} diff --git a/tests/bwameth_run_qualimap.nf.test b/tests/bwameth_run_qualimap.nf.test new file mode 100644 index 00000000..37884096 --- /dev/null +++ b/tests/bwameth_run_qualimap.nf.test @@ -0,0 +1,42 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + tag "cpu" + + test("Params: bwameth | run_qualimap") { + when { + params { + aligner = "bwameth" + outdir = "$outputDir" + run_qualimap = true + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bwameth_run_qualimap.nf.test.snap b/tests/bwameth_run_qualimap.nf.test.snap new file mode 100644 index 00000000..c5aa4055 --- /dev/null +++ b/tests/bwameth_run_qualimap.nf.test.snap @@ -0,0 +1,482 @@ +{ + "Params: bwameth | run_qualimap": { + "content": [ + 51, + { + "BWAMETH_ALIGN": { + "bwameth": "0.2.7" + }, + "BWAMETH_INDEX": { + "bwameth": "0.2.7" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + "GUNZIP": { + "gunzip": 1.1 + }, + "QUALIMAP_BAMQC": { + "qualimap": 2.3 + }, + "TRIMGALORE": { + "trimgalore": "0.6.10", + "cutadapt": 4.9, + "pigz": 2.8 + }, + "Workflow": { + "nf-core/methylseq": "v3.0.0" + } + }, + [ + "bwameth", + 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}, + "timestamp": "2024-12-12T06:46:41.632218793" + } +} diff --git a/tests/bwameth_save_reference_save_align_intermeds.nf.test b/tests/bwameth_save_reference_save_align_intermeds.nf.test index 2ce41cd3..52258501 100644 --- a/tests/bwameth_save_reference_save_align_intermeds.nf.test +++ b/tests/bwameth_save_reference_save_align_intermeds.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bwameth | save_reference | save_align_intermeds") { when { @@ -27,7 +28,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap index 19d1a27e..f7d7f4c5 100644 --- a/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap +++ b/tests/bwameth_save_reference_save_align_intermeds.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bwameth | save_reference | save_align_intermeds": { "content": [ - 50, + 47, { "BWAMETH_ALIGN": { "bwameth": "0.2.7" @@ -12,32 +12,33 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ "bwameth", "bwameth/alignments", "bwameth/alignments/Ecoli_10K_methylated.bam", - "bwameth/alignments/Ecoli_10K_methylated.sorted.bam", - "bwameth/alignments/Ecoli_10K_methylated.sorted.bam.bai", + "bwameth/alignments/Ecoli_10K_methylated.deduplicated.sorted.bam", + "bwameth/alignments/Ecoli_10K_methylated.deduplicated.sorted.bam.bai", "bwameth/alignments/SRR389222_sub1.bam", - "bwameth/alignments/SRR389222_sub1.sorted.bam", - "bwameth/alignments/SRR389222_sub1.sorted.bam.bai", + "bwameth/alignments/SRR389222_sub1.deduplicated.sorted.bam", + "bwameth/alignments/SRR389222_sub1.deduplicated.sorted.bam.bai", "bwameth/alignments/SRR389222_sub2.bam", - "bwameth/alignments/SRR389222_sub2.sorted.bam", - "bwameth/alignments/SRR389222_sub2.sorted.bam.bai", + "bwameth/alignments/SRR389222_sub2.deduplicated.sorted.bam", + "bwameth/alignments/SRR389222_sub2.deduplicated.sorted.bam.bai", "bwameth/alignments/SRR389222_sub3.bam", - "bwameth/alignments/SRR389222_sub3.sorted.bam", - "bwameth/alignments/SRR389222_sub3.sorted.bam.bai", + "bwameth/alignments/SRR389222_sub3.deduplicated.sorted.bam", + "bwameth/alignments/SRR389222_sub3.deduplicated.sorted.bam.bai", "bwameth/alignments/samtools_stats", "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.flagstat", "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.stats", @@ -48,12 +49,16 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", + "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -115,7 +120,6 @@ "multiqc/bwameth/multiqc_data/multiqc_fastqc.txt", "multiqc/bwameth/multiqc_data/multiqc_general_stats.txt", "multiqc/bwameth/multiqc_data/multiqc_picard_dups.txt", - "multiqc/bwameth/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bwameth/multiqc_data/multiqc_samtools_flagstat.txt", "multiqc/bwameth/multiqc_data/multiqc_samtools_stats.txt", "multiqc/bwameth/multiqc_data/multiqc_software_versions.txt", @@ -124,10 +128,6 @@ "multiqc/bwameth/multiqc_data/picard_histogram.txt", "multiqc/bwameth/multiqc_data/picard_histogram_1.txt", "multiqc/bwameth/multiqc_data/picard_histogram_2.txt", - "multiqc/bwameth/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bwameth/multiqc_data/qualimap_gc_content.txt", - "multiqc/bwameth/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bwameth/multiqc_data/qualimap_insert_size.txt", "multiqc/bwameth/multiqc_data/samtools-flagstat-dp_Percentage_of_total.txt", "multiqc/bwameth/multiqc_data/samtools-flagstat-dp_Read_counts.txt", "multiqc/bwameth/multiqc_data/samtools-stats-dp.txt", @@ -153,10 +153,6 @@ "multiqc/bwameth/multiqc_plots/pdf/general_stats_table.pdf", "multiqc/bwameth/multiqc_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/bwameth/multiqc_plots/pdf/picard_deduplication-pct.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-stats-dp.pdf", @@ -182,10 +178,6 @@ "multiqc/bwameth/multiqc_plots/png/general_stats_table.png", "multiqc/bwameth/multiqc_plots/png/picard_deduplication-cnt.png", "multiqc/bwameth/multiqc_plots/png/picard_deduplication-pct.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bwameth/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/bwameth/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/bwameth/multiqc_plots/png/samtools-stats-dp.png", @@ -211,10 +203,6 @@ "multiqc/bwameth/multiqc_plots/svg/general_stats_table.svg", "multiqc/bwameth/multiqc_plots/svg/picard_deduplication-cnt.svg", "multiqc/bwameth/multiqc_plots/svg/picard_deduplication-pct.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_coverage_histogram.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_gc_content.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_genome_fraction.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_insert_size.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-stats-dp.svg", @@ -222,146 +210,7 @@ "multiqc/bwameth/multiqc_plots/svg/samtools_alignment_plot-pct.svg", "multiqc/bwameth/multiqc_report.html", "pipeline_info", - "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", - "qualimap", - "qualimap/Ecoli_10K_methylated", - "qualimap/Ecoli_10K_methylated/css", - "qualimap/Ecoli_10K_methylated/css/agogo.css", - "qualimap/Ecoli_10K_methylated/css/ajax-loader.gif", - "qualimap/Ecoli_10K_methylated/css/basic.css", - "qualimap/Ecoli_10K_methylated/css/bgfooter.png", - "qualimap/Ecoli_10K_methylated/css/bgtop.png", - "qualimap/Ecoli_10K_methylated/css/comment-bright.png", - "qualimap/Ecoli_10K_methylated/css/comment-close.png", - "qualimap/Ecoli_10K_methylated/css/comment.png", - "qualimap/Ecoli_10K_methylated/css/doctools.js", - "qualimap/Ecoli_10K_methylated/css/down-pressed.png", - "qualimap/Ecoli_10K_methylated/css/down.png", - "qualimap/Ecoli_10K_methylated/css/file.png", - "qualimap/Ecoli_10K_methylated/css/jquery.js", - "qualimap/Ecoli_10K_methylated/css/minus.png", - "qualimap/Ecoli_10K_methylated/css/plus.png", - "qualimap/Ecoli_10K_methylated/css/pygments.css", - "qualimap/Ecoli_10K_methylated/css/qualimap_logo_small.png", - "qualimap/Ecoli_10K_methylated/css/report.css", - "qualimap/Ecoli_10K_methylated/css/searchtools.js", - "qualimap/Ecoli_10K_methylated/css/underscore.js", - "qualimap/Ecoli_10K_methylated/css/up-pressed.png", - "qualimap/Ecoli_10K_methylated/css/up.png", - "qualimap/Ecoli_10K_methylated/css/websupport.js", - 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"SRR389222_sub1.stats:md5,0f660ccc767662d4bd8c5197f3d46a87", + "SRR389222_sub1.stats:md5,21e116cc6374c4a2d55d2c383cd4281e", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,9343b74f4d825bfb2a554be3d8bed432", + "SRR389222_sub2.stats:md5,75cb0f1e953843150e3b217ec3f271da", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,f41e135f71893e2a8b589c4a66cbfeec", + "SRR389222_sub3.stats:md5,6876e424094ecdf302bd2097f8e21b1c", "genome.fa.bwameth.c2t:md5,e51d48ed28fa0c26e2f9c9f13d09403b", "genome.fa.bwameth.c2t.amb:md5,010a242c6764efb30141868a45d698b3", "genome.fa.bwameth.c2t.ann:md5,09b4db3d87a2d4dac9e10e807f377110", @@ -419,27 +268,19 @@ "fastqc_sequence_counts_plot.txt:md5,58eeeb06bc9dcc1764c7daf0847d6bbf", "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", - "multiqc_citations.txt:md5,581df5b266851d0244e7cfb213351ffb", + "multiqc_citations.txt:md5,ad6c1e326b4276501a3b42eaad747de1", "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "multiqc_picard_dups.txt:md5,82eaab96189f22fd93db38bb516ba6a5", "multiqc_samtools_flagstat.txt:md5,a8f5b45b8b3412a9adc3dd0d35208c73", - "multiqc_samtools_stats.txt:md5,e24271a8111b06c1f545b6b1a077a4a7", + "multiqc_samtools_stats.txt:md5,bfcab6a9bd26872ecd2ec469d222c70b", "picard_deduplication.txt:md5,7dacf4d4e0d7d2d9a7205beecfa7125c", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "qualimap_coverage_histogram.txt:md5,c7c932e4d84b735bd434c1aaa713b6e6", - "qualimap_gc_content.txt:md5,893d1acba7a6675ff9e2eff2985fa4e3", - "qualimap_genome_fraction.txt:md5,ef5b6010b52a03f6e58356db7128d0dc", - "qualimap_insert_size.txt:md5,f86cc9fe7a12af8f62f26312660e9225", "samtools-flagstat-dp_Percentage_of_total.txt:md5,ff5d65a480449ba98587c43f3a2bd33e", "samtools-flagstat-dp_Read_counts.txt:md5,6a5332e2ad59f7da00b5a9a1a25fd2f8", "samtools-stats-dp.txt:md5,52021b9a9455b39b39dd357bc2e8d346", - "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b", - "genome_results.txt:md5,1ee2e29ac41c2cd7e6a0f00741e8d16e", - "genome_results.txt:md5,2c755b15ae5ad4a1d29395320a6264ca", - "genome_results.txt:md5,2294badeccd2e8870fd6c60d115687b0", - "genome_results.txt:md5,4da1144933d094185d02f7482c120804" + "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b" ], [ [ @@ -447,7 +288,7 @@ "4a9ba2169facef4ed3d92d539c8c78af" ], [ - "Ecoli_10K_methylated.sorted.bam", + "Ecoli_10K_methylated.deduplicated.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], [ @@ -455,7 +296,7 @@ "e50275d6d44138f19d65ee479444d5ce" ], [ - "SRR389222_sub1.sorted.bam", + "SRR389222_sub1.deduplicated.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], [ @@ -463,7 +304,7 @@ "d365b8b2662b2abffb51dd67a1f463b4" ], [ - "SRR389222_sub2.sorted.bam", + "SRR389222_sub2.deduplicated.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], [ @@ -471,21 +312,37 @@ "a9fd2900b9d759f8f4f62cbbb2744fde" ], [ - "SRR389222_sub3.sorted.bam", + "SRR389222_sub3.deduplicated.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" ], + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "a2921f761f431ede522016f83f75c12d" + ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "a2921f761f431ede522016f83f75c12d" ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "e50275d6d44138f19d65ee479444d5ce" + ], [ "SRR389222_sub1.markdup.sorted.bam", "e50275d6d44138f19d65ee479444d5ce" ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "d365b8b2662b2abffb51dd67a1f463b4" + ], [ "SRR389222_sub2.markdup.sorted.bam", "d365b8b2662b2abffb51dd67a1f463b4" ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "a9fd2900b9d759f8f4f62cbbb2744fde" + ], [ "SRR389222_sub3.markdup.sorted.bam", "a9fd2900b9d759f8f4f62cbbb2744fde" @@ -493,9 +350,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:44:54.756005023" + "timestamp": "2024-12-12T06:48:21.201464769" } -} \ No newline at end of file +} diff --git a/tests/bwameth_skip_deduplication.nf.test b/tests/bwameth_skip_deduplication.nf.test index 0b208bf4..66a4e910 100644 --- a/tests/bwameth_skip_deduplication.nf.test +++ b/tests/bwameth_skip_deduplication.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bwameth | skip_deduplication") { when { @@ -26,7 +27,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bwameth_skip_deduplication.nf.test.snap b/tests/bwameth_skip_deduplication.nf.test.snap index a646e5d7..abdf69c6 100644 --- a/tests/bwameth_skip_deduplication.nf.test.snap +++ b/tests/bwameth_skip_deduplication.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bwameth | skip_deduplication": { "content": [ - 42, + 39, { "BWAMETH_ALIGN": { "bwameth": "0.2.7" @@ -12,20 +12,25 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ "bwameth", "bwameth/alignments", + "bwameth/alignments/Ecoli_10K_methylated.sorted.bam", + "bwameth/alignments/SRR389222_sub1.sorted.bam", + "bwameth/alignments/SRR389222_sub2.sorted.bam", + "bwameth/alignments/SRR389222_sub3.sorted.bam", "bwameth/alignments/samtools_stats", "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.flagstat", "bwameth/alignments/samtools_stats/Ecoli_10K_methylated.stats", @@ -35,6 +40,7 @@ "bwameth/alignments/samtools_stats/SRR389222_sub2.stats", "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", + "bwameth/deduplicated", "fastqc", "fastqc/Ecoli_10K_methylated_1_fastqc.html", "fastqc/Ecoli_10K_methylated_2_fastqc.html", @@ -80,15 +86,10 @@ "multiqc/bwameth/multiqc_data/multiqc_data.json", "multiqc/bwameth/multiqc_data/multiqc_fastqc.txt", "multiqc/bwameth/multiqc_data/multiqc_general_stats.txt", - "multiqc/bwameth/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bwameth/multiqc_data/multiqc_samtools_flagstat.txt", "multiqc/bwameth/multiqc_data/multiqc_samtools_stats.txt", "multiqc/bwameth/multiqc_data/multiqc_software_versions.txt", "multiqc/bwameth/multiqc_data/multiqc_sources.txt", - "multiqc/bwameth/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bwameth/multiqc_data/qualimap_gc_content.txt", - "multiqc/bwameth/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bwameth/multiqc_data/qualimap_insert_size.txt", "multiqc/bwameth/multiqc_data/samtools-flagstat-dp_Percentage_of_total.txt", "multiqc/bwameth/multiqc_data/samtools-flagstat-dp_Read_counts.txt", "multiqc/bwameth/multiqc_data/samtools-stats-dp.txt", @@ -112,10 +113,6 @@ "multiqc/bwameth/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", "multiqc/bwameth/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", "multiqc/bwameth/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-stats-dp.pdf", @@ -139,10 +136,6 @@ "multiqc/bwameth/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/bwameth/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/bwameth/multiqc_plots/png/general_stats_table.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bwameth/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/bwameth/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/bwameth/multiqc_plots/png/samtools-stats-dp.png", @@ -166,10 +159,6 @@ "multiqc/bwameth/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/bwameth/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/bwameth/multiqc_plots/svg/general_stats_table.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_coverage_histogram.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_gc_content.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_genome_fraction.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_insert_size.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-stats-dp.svg", @@ -177,146 +166,7 @@ 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"trimgalore", "trimgalore/fastqc", "trimgalore/fastqc/Ecoli_10K_methylated_1_val_1_fastqc.html", @@ -339,13 +189,13 @@ ], [ "Ecoli_10K_methylated.flagstat:md5,f520e87cc4050799a0dbed72909572ec", - "Ecoli_10K_methylated.stats:md5,2df1b94e099f2948ad990224f7cf07a4", + "Ecoli_10K_methylated.stats:md5,48d2b9fa62581706d67b027138cff41e", "SRR389222_sub1.flagstat:md5,ad8159a7683b9c3057bf54ccb77a2ddc", - "SRR389222_sub1.stats:md5,0f660ccc767662d4bd8c5197f3d46a87", + "SRR389222_sub1.stats:md5,a578019df62d8ae1e4976f20ac1c7993", "SRR389222_sub2.flagstat:md5,e768b4f54014d62b096152c44f920bc1", - "SRR389222_sub2.stats:md5,9343b74f4d825bfb2a554be3d8bed432", + "SRR389222_sub2.stats:md5,b60c66a26f2c346cbb85fb59c8de392b", "SRR389222_sub3.flagstat:md5,39516f7d2c77e6fef9543edf8cddbcd6", - "SRR389222_sub3.stats:md5,f41e135f71893e2a8b589c4a66cbfeec", + "SRR389222_sub3.stats:md5,cf3e88bd028b048c6f6a416eacef6a1b", "Ecoli_10K_methylated.sorted_CpG.bedGraph:md5,aa88f19284e63097e9abccac4d7c6669", "SRR389222_sub1.sorted_CpG.bedGraph:md5,4475a9462ce86a019015b69b82a9d5a2", "SRR389222_sub2.sorted_CpG.bedGraph:md5,18b8845d9d985d3c203ca6c9c40aab1b", @@ -368,31 +218,38 @@ "fastqc_sequence_counts_plot.txt:md5,58eeeb06bc9dcc1764c7daf0847d6bbf", "fastqc_sequence_duplication_levels_plot.txt:md5,9e5712db9aa39b5754ea1e0c49cfff15", "fastqc_top_overrepresented_sequences_table.txt:md5,6dfc5334a09c05392ea17369aa742d01", - "multiqc_citations.txt:md5,581df5b266851d0244e7cfb213351ffb", + "multiqc_citations.txt:md5,ad6c1e326b4276501a3b42eaad747de1", "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", "multiqc_samtools_flagstat.txt:md5,a8f5b45b8b3412a9adc3dd0d35208c73", - "multiqc_samtools_stats.txt:md5,e24271a8111b06c1f545b6b1a077a4a7", - "qualimap_coverage_histogram.txt:md5,c7c932e4d84b735bd434c1aaa713b6e6", - "qualimap_gc_content.txt:md5,893d1acba7a6675ff9e2eff2985fa4e3", - "qualimap_genome_fraction.txt:md5,ef5b6010b52a03f6e58356db7128d0dc", - "qualimap_insert_size.txt:md5,f86cc9fe7a12af8f62f26312660e9225", + "multiqc_samtools_stats.txt:md5,bfcab6a9bd26872ecd2ec469d222c70b", "samtools-flagstat-dp_Percentage_of_total.txt:md5,ff5d65a480449ba98587c43f3a2bd33e", "samtools-flagstat-dp_Read_counts.txt:md5,6a5332e2ad59f7da00b5a9a1a25fd2f8", "samtools-stats-dp.txt:md5,52021b9a9455b39b39dd357bc2e8d346", - "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b", - "genome_results.txt:md5,2dc1bce48dc3554b990674d421287366", - "genome_results.txt:md5,ed81b2fd10b2c548610d546b4e4d3b76", - "genome_results.txt:md5,92485f8ac205d7fa1140cdc293f07560", - "genome_results.txt:md5,478f711b8ef22e094e4d0ff7fa0dfda0" + "samtools_alignment_plot.txt:md5,39f42e039f96cc2b17248b44ccaf425b" ], [ - + [ + "Ecoli_10K_methylated.sorted.bam", + "a2921f761f431ede522016f83f75c12d" + ], + [ + "SRR389222_sub1.sorted.bam", + "e50275d6d44138f19d65ee479444d5ce" + ], + [ + "SRR389222_sub2.sorted.bam", + "d365b8b2662b2abffb51dd67a1f463b4" + ], + [ + "SRR389222_sub3.sorted.bam", + "a9fd2900b9d759f8f4f62cbbb2744fde" + ] ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:46:02.99245907" + "timestamp": "2024-12-12T06:49:39.523045474" } -} \ No newline at end of file +} diff --git a/tests/bwameth_skip_trimming.nf.test b/tests/bwameth_skip_trimming.nf.test index 3b01599d..5ec570ec 100644 --- a/tests/bwameth_skip_trimming.nf.test +++ b/tests/bwameth_skip_trimming.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: bwameth | skip_trimming") { when { @@ -26,7 +27,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/bwameth_skip_trimming.nf.test.snap b/tests/bwameth_skip_trimming.nf.test.snap index 8e890b74..68e34400 100644 --- a/tests/bwameth_skip_trimming.nf.test.snap +++ b/tests/bwameth_skip_trimming.nf.test.snap @@ -1,7 +1,7 @@ { "Params: bwameth | skip_trimming": { "content": [ - 46, + 43, { "BWAMETH_ALIGN": { "bwameth": "0.2.7" @@ -12,11 +12,11 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ @@ -32,12 +32,16 @@ "bwameth/alignments/samtools_stats/SRR389222_sub3.flagstat", "bwameth/alignments/samtools_stats/SRR389222_sub3.stats", "bwameth/deduplicated", + "bwameth/deduplicated/Ecoli_10K_methylated.deduplicated.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam", "bwameth/deduplicated/Ecoli_10K_methylated.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub1.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub1.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub2.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub2.markdup.sorted.bam.bai", + "bwameth/deduplicated/SRR389222_sub3.deduplicated.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam", "bwameth/deduplicated/SRR389222_sub3.markdup.sorted.bam.bai", "bwameth/deduplicated/picard_metrics", @@ -87,7 +91,6 @@ "multiqc/bwameth/multiqc_data/multiqc_fastqc.txt", "multiqc/bwameth/multiqc_data/multiqc_general_stats.txt", "multiqc/bwameth/multiqc_data/multiqc_picard_dups.txt", - "multiqc/bwameth/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bwameth/multiqc_data/multiqc_samtools_flagstat.txt", "multiqc/bwameth/multiqc_data/multiqc_samtools_stats.txt", "multiqc/bwameth/multiqc_data/multiqc_software_versions.txt", @@ -96,10 +99,6 @@ "multiqc/bwameth/multiqc_data/picard_histogram.txt", "multiqc/bwameth/multiqc_data/picard_histogram_1.txt", "multiqc/bwameth/multiqc_data/picard_histogram_2.txt", - "multiqc/bwameth/multiqc_data/qualimap_coverage_histogram.txt", - "multiqc/bwameth/multiqc_data/qualimap_gc_content.txt", - "multiqc/bwameth/multiqc_data/qualimap_genome_fraction.txt", - "multiqc/bwameth/multiqc_data/qualimap_insert_size.txt", "multiqc/bwameth/multiqc_data/samtools-flagstat-dp_Percentage_of_total.txt", "multiqc/bwameth/multiqc_data/samtools-flagstat-dp_Read_counts.txt", "multiqc/bwameth/multiqc_data/samtools-stats-dp.txt", @@ -121,10 +120,6 @@ "multiqc/bwameth/multiqc_plots/pdf/general_stats_table.pdf", "multiqc/bwameth/multiqc_plots/pdf/picard_deduplication-cnt.pdf", "multiqc/bwameth/multiqc_plots/pdf/picard_deduplication-pct.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_coverage_histogram.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_gc_content.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_genome_fraction.pdf", - "multiqc/bwameth/multiqc_plots/pdf/qualimap_insert_size.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/bwameth/multiqc_plots/pdf/samtools-stats-dp.pdf", @@ -146,10 +141,6 @@ "multiqc/bwameth/multiqc_plots/png/general_stats_table.png", "multiqc/bwameth/multiqc_plots/png/picard_deduplication-cnt.png", "multiqc/bwameth/multiqc_plots/png/picard_deduplication-pct.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bwameth/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bwameth/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/bwameth/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/bwameth/multiqc_plots/png/samtools-stats-dp.png", @@ -171,10 +162,6 @@ "multiqc/bwameth/multiqc_plots/svg/general_stats_table.svg", "multiqc/bwameth/multiqc_plots/svg/picard_deduplication-cnt.svg", "multiqc/bwameth/multiqc_plots/svg/picard_deduplication-pct.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_coverage_histogram.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_gc_content.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_genome_fraction.svg", - "multiqc/bwameth/multiqc_plots/svg/qualimap_insert_size.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/bwameth/multiqc_plots/svg/samtools-stats-dp.svg", @@ -182,156 +169,17 @@ "multiqc/bwameth/multiqc_plots/svg/samtools_alignment_plot-pct.svg", "multiqc/bwameth/multiqc_report.html", "pipeline_info", - "pipeline_info/nf_core_pipeline_software_mqc_versions.yml", - "qualimap", - "qualimap/Ecoli_10K_methylated", - "qualimap/Ecoli_10K_methylated/css", - "qualimap/Ecoli_10K_methylated/css/agogo.css", - "qualimap/Ecoli_10K_methylated/css/ajax-loader.gif", - "qualimap/Ecoli_10K_methylated/css/basic.css", - "qualimap/Ecoli_10K_methylated/css/bgfooter.png", - "qualimap/Ecoli_10K_methylated/css/bgtop.png", - "qualimap/Ecoli_10K_methylated/css/comment-bright.png", - "qualimap/Ecoli_10K_methylated/css/comment-close.png", - "qualimap/Ecoli_10K_methylated/css/comment.png", - "qualimap/Ecoli_10K_methylated/css/doctools.js", - "qualimap/Ecoli_10K_methylated/css/down-pressed.png", - "qualimap/Ecoli_10K_methylated/css/down.png", - "qualimap/Ecoli_10K_methylated/css/file.png", - 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"genome_results.txt:md5,b7376228bb23c9133fed45b95c60d082" + "samtools_alignment_plot.txt:md5,fe4c9af19d69c3982b75ad458a1a9148" ], [ + [ + "Ecoli_10K_methylated.deduplicated.sorted.bam", + "5b485bcabdb1ad5955cfa061741fad31" + ], [ "Ecoli_10K_methylated.markdup.sorted.bam", "5b485bcabdb1ad5955cfa061741fad31" ], + [ + "SRR389222_sub1.deduplicated.sorted.bam", + "37ec1c6338cc3fee7ab1cb2d48dba38" + ], [ "SRR389222_sub1.markdup.sorted.bam", "37ec1c6338cc3fee7ab1cb2d48dba38" ], + [ + "SRR389222_sub2.deduplicated.sorted.bam", + "783d3be6b5bfa58142c3dbe864f6d8c5" + ], [ "SRR389222_sub2.markdup.sorted.bam", "783d3be6b5bfa58142c3dbe864f6d8c5" ], + [ + "SRR389222_sub3.deduplicated.sorted.bam", + "4bbaef9917f4ff0248d1f5853f583fd0" + ], [ "SRR389222_sub3.markdup.sorted.bam", "4bbaef9917f4ff0248d1f5853f583fd0" @@ -392,9 +248,9 @@ ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-17T10:43:35.237760512" + "timestamp": "2024-12-04T04:44:20.47452156" } } diff --git a/tests/bwameth_use_gpu.nf.test b/tests/bwameth_use_gpu.nf.test new file mode 100644 index 00000000..da89ea3c --- /dev/null +++ b/tests/bwameth_use_gpu.nf.test @@ -0,0 +1,43 @@ +nextflow_pipeline { + + name "Test Workflow main.nf" + script "../main.nf" + config "./nextflow.config" + tag "gpu" + + test("Params: bwameth | use_gpu") { + when { + params { + input = "${projectDir}/assets/samplesheet_gpu.csv" + aligner = "bwameth" // uses parabricks/fq2bammeth + use_gpu = true + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), + // All stable path name + stable_name, + // All files with stable contents + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } + ).match() } + ) + } + } + +} diff --git a/tests/bwameth_use_gpu.nf.test.snap b/tests/bwameth_use_gpu.nf.test.snap new file mode 100644 index 00000000..176d3108 --- /dev/null +++ b/tests/bwameth_use_gpu.nf.test.snap @@ -0,0 +1,255 @@ +{ + "Params: bwameth | use_gpu": { + "content": [ + 36, + { + "BWAMETH_INDEX": { + "bwameth": "0.2.7" + }, + "FASTQC": { + "fastqc": "0.12.1" + }, + 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b/tests/default.nf.test index 6a210a07..60a4885d 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test Workflow main.nf" script "../main.nf" config "./nextflow.config" + tag "cpu" test("Params: default") { when { @@ -24,7 +25,7 @@ nextflow_pipeline { // Number of tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_methylseq_software_mqc_versions.yml"), // All stable path name stable_name, // All files with stable contents diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index f38b3782..2f84d4c0 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,17 +1,17 @@ { "Params: default with bowtie2-index": { "content": [ - 43 + 36 ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-12T07:51:49.810650315" + "timestamp": "2024-11-27T17:37:46.406666357" }, "Params: default": { "content": [ - 43, + 36, { "BISMARK_ALIGN": { "bismark": "0.24.2" @@ -22,15 +22,16 @@ "FASTQC": { "fastqc": "0.12.1" }, - "QUALIMAP_BAMQC": { - "qualimap": 2.3 + "GUNZIP": { + "gunzip": 1.1 }, "TRIMGALORE": { "trimgalore": "0.6.10", - "cutadapt": 4.9 + "cutadapt": 4.9, + "pigz": 2.8 }, "Workflow": { - "nf-core/methylseq": "v2.7.1" + "nf-core/methylseq": "v3.0.0" } }, [ @@ -157,13 +158,8 @@ "multiqc/bismark/multiqc_data/multiqc_data.json", "multiqc/bismark/multiqc_data/multiqc_fastqc.txt", "multiqc/bismark/multiqc_data/multiqc_general_stats.txt", - "multiqc/bismark/multiqc_data/multiqc_qualimap_bamqc_genome_results.txt", "multiqc/bismark/multiqc_data/multiqc_software_versions.txt", "multiqc/bismark/multiqc_data/multiqc_sources.txt", - 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"multiqc/bismark/multiqc_plots/png/bismark_alignment-cnt.png", @@ -231,10 +223,6 @@ "multiqc/bismark/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", "multiqc/bismark/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", "multiqc/bismark/multiqc_plots/png/general_stats_table.png", - "multiqc/bismark/multiqc_plots/png/qualimap_coverage_histogram.png", - "multiqc/bismark/multiqc_plots/png/qualimap_gc_content.png", - "multiqc/bismark/multiqc_plots/png/qualimap_genome_fraction.png", - "multiqc/bismark/multiqc_plots/png/qualimap_insert_size.png", "multiqc/bismark/multiqc_plots/svg", "multiqc/bismark/multiqc_plots/svg/bismark-methylation-dp.svg", "multiqc/bismark/multiqc_plots/svg/bismark_alignment-cnt.svg", @@ -266,204 +254,9 @@ "multiqc/bismark/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", "multiqc/bismark/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", "multiqc/bismark/multiqc_plots/svg/general_stats_table.svg", - 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"multiqc_bismark_methextract.txt:md5,825f57cdf45203406e583beb495afccc", - "multiqc_citations.txt:md5,b9d42869faad581bd963d3d3bb490026", - "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732", - "qualimap_coverage_histogram.txt:md5,7cd194077fe839edf034b44cc73dd024", - "qualimap_gc_content.txt:md5,4f6ec70d9fb71ffe5f2f99f44fe5ef0c", - "qualimap_genome_fraction.txt:md5,3e528946a376ae752b57adaaa73f5cdf", - "qualimap_insert_size.txt:md5,8327f805cbaf1c61ca3128b6c16c7dfd", - "genome_results.txt:md5,e2a57140a56e0e4a1905c70084ccbb41", - "genome_results.txt:md5,69a3dc8568127c50b0decb29757230ee", - "genome_results.txt:md5,13d933d61649b837de72a418d5126c1b", - "genome_results.txt:md5,235830239cfc43d8e84c049b1e9b180a" + "multiqc_citations.txt:md5,73a6d29705d5a07f17f99c92e3a0f148", + "multiqc_cutadapt.txt:md5,883891ac4901385102be053212068732" ], [ [ @@ -583,9 +368,9 @@ ] ], "meta": { - "nf-test": "0.9.1", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.2" }, - "timestamp": "2024-10-25T14:48:27.537789856" + "timestamp": "2024-12-12T06:55:35.766947967" } -} \ No newline at end of file +} diff --git a/tests/nextflow.config b/tests/nextflow.config index 794a5cb8..6b64038a 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -8,31 +8,27 @@ params { // Base directory for nf-core/modules test data modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/' // Base directory for nf-core/methylseq test data - pipelines_testdata_base_path = 'https://github.com/nf-core/test-datasets/raw/methylseq/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/methylseq/' // Input data input = "${projectDir}/assets/samplesheet.csv" - fasta = "${params.pipelines_testdata_base_path}/reference/genome.fa" + fasta = "${params.pipelines_testdata_base_path}/reference/genome.fa.gz" fasta_index = "${params.pipelines_testdata_base_path}/reference/genome.fa.fai" outdir = 'results' } // Impose sensible resource limits for testing process { - withName: '.*' { - cpus = 2 - memory = 3.GB - time = 2.h - } - - withName: PRESEQ_LCEXTRAP { - errorStrategy = 'ignore' - } + resourceLimits = [ + cpus: 2, + memory: '3.GB', + time: '2.h' + ] } // Impose same minimum Nextflow version as the pipeline for testing manifest { - nextflowVersion = '!>=24.04.2' + nextflowVersion = '!>=24.10.2' } // Disable all Nextflow reporting options diff --git a/workflows/methylseq/main.nf b/workflows/methylseq/main.nf index 0cb93f59..d43ac39e 100644 --- a/workflows/methylseq/main.nf +++ b/workflows/methylseq/main.nf @@ -4,20 +4,19 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - -include { FASTQC } from '../../modules/nf-core/fastqc/main' -include { TRIMGALORE } from '../../modules/nf-core/trimgalore/main' -include { QUALIMAP_BAMQC } from '../../modules/nf-core/qualimap/bamqc/main' -include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap/main' -include { MULTIQC } from '../../modules/nf-core/multiqc/main' -include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main' -include { paramsSummaryMap } from 'plugin/nf-schema' -include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' -include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' -include { validateInputSamplesheet } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' -include { BISMARK } from '../../subworkflows/local/bismark/' -include { BWAMETH } from '../../subworkflows/local/bwameth' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { FASTQC } from '../../modules/nf-core/fastqc/main' +include { TRIMGALORE } from '../../modules/nf-core/trimgalore/main' +include { QUALIMAP_BAMQC } from '../../modules/nf-core/qualimap/bamqc/main' +include { PRESEQ_LCEXTRAP } from '../../modules/nf-core/preseq/lcextrap/main' +include { MULTIQC } from '../../modules/nf-core/multiqc/main' +include { CAT_FASTQ } from '../../modules/nf-core/cat/fastq/main' +include { FASTQ_ALIGN_DEDUP_BISMARK } from '../../subworkflows/nf-core/fastq_align_dedup_bismark/main' +include { FASTQ_ALIGN_DEDUP_BWAMETH } from '../../subworkflows/nf-core/fastq_align_dedup_bwameth/main' +include { paramsSummaryMultiqc } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { softwareVersionsToYAML } from '../../subworkflows/nf-core/utils_nfcore_pipeline' +include { methodsDescriptionText } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' +include { validateInputSamplesheet } from '../../subworkflows/local/utils_nfcore_methylseq_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -28,54 +27,67 @@ include { BWAMETH } from '../../subworkflows/local/bwameth' workflow METHYLSEQ { take: - samplesheet // channel: samplesheet read in from --input - ch_versions // channel: [ path(versions.yml) ] - ch_fasta // channel: path(genome.fasta) - ch_fasta_index // channel: path(star/index/) - ch_bismark_index // channel: path(star/index/) - ch_bwameth_index // channel: path(star/index/) + samplesheet // channel: [ path(samplesheet.csv) ] + ch_versions // channel: [ path(versions.yml) ] + ch_fasta // channel: [ path(fasta) ] + ch_fasta_index // channel: [ path(fasta index) ] + ch_bismark_index // channel: [ path(bismark index) ] + ch_bwameth_index // channel: [ path(bwameth index) ] main: + ch_fastq = Channel.empty() + ch_fastqc_html = Channel.empty() + ch_fastqc_zip = Channel.empty() + ch_reads = Channel.empty() + ch_bam = Channel.empty() + ch_bai = Channel.empty() + ch_qualimap = Channel.empty() + ch_preseq = Channel.empty() ch_multiqc_files = Channel.empty() // // Branch channels from input samplesheet channel // - samplesheet - .branch { meta, fastqs -> - single : fastqs.size() == 1 - return [ meta, fastqs.flatten() ] - multiple: fastqs.size() > 1 - return [ meta, fastqs.flatten() ] - } - .set { ch_samplesheet } + ch_samplesheet = samplesheet + .branch { meta, fastqs -> + single : fastqs.size() == 1 + return [ meta, fastqs.flatten() ] + multiple: fastqs.size() > 1 + return [ meta, fastqs.flatten() ] + } // // MODULE: Concatenate FastQ files from same sample if required // - CAT_FASTQ (ch_samplesheet.multiple) - .reads - .mix(ch_samplesheet.single) - .set {ch_fastq} + CAT_FASTQ ( + ch_samplesheet.multiple + ) + ch_fastq = CAT_FASTQ.out.reads.mix(ch_samplesheet.single) ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) // // MODULE: Run FastQC // - FASTQC (ch_fastq) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + FASTQC ( + ch_fastq + ) + ch_fastqc_html = FASTQC.out.html + ch_fastqc_zip = FASTQC.out.zip + ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{ meta, zip -> zip }) + ch_versions = ch_versions.mix(FASTQC.out.versions.first()) // // MODULE: Run TrimGalore! // if (!params.skip_trimming) { - TRIMGALORE(ch_fastq) - reads = TRIMGALORE.out.reads + TRIMGALORE( + ch_fastq + ) + ch_reads = TRIMGALORE.out.reads ch_versions = ch_versions.mix(TRIMGALORE.out.versions.first()) } else { - reads = ch_fastq + ch_reads = ch_fastq } // @@ -83,63 +95,73 @@ workflow METHYLSEQ { // // Aligner: bismark or bismark_hisat - if( params.aligner =~ /bismark/ ){ + if ( params.aligner =~ /bismark/ ) { // // Run Bismark alignment + downstream processing // - BISMARK ( - reads, + FASTQ_ALIGN_DEDUP_BISMARK ( + ch_reads, ch_fasta, ch_bismark_index, params.skip_deduplication || params.rrbs, params.cytosine_report || params.nomeseq ) - ch_versions = ch_versions.mix(BISMARK.out.versions.unique{ it.baseName }) - ch_bam = BISMARK.out.bam - ch_dedup = BISMARK.out.dedup - ch_aligner_mqc = BISMARK.out.mqc + ch_bam = FASTQ_ALIGN_DEDUP_BISMARK.out.bam + ch_bai = FASTQ_ALIGN_DEDUP_BISMARK.out.bai + ch_aligner_mqc = FASTQ_ALIGN_DEDUP_BISMARK.out.multiqc + ch_versions = ch_versions.mix(FASTQ_ALIGN_DEDUP_BISMARK.out.versions.unique{ it.baseName }) } // Aligner: bwameth else if ( params.aligner == 'bwameth' ){ - BWAMETH ( - reads, - ch_bwameth_index, + FASTQ_ALIGN_DEDUP_BWAMETH ( + ch_reads, ch_fasta, - ch_fasta_index, + ch_fasta_index.map{ index -> [ [:], index ]}, + ch_bwameth_index, params.skip_deduplication || params.rrbs, ) - ch_versions = ch_versions.mix(BWAMETH.out.versions.unique{ it.baseName }) - ch_bam = BWAMETH.out.bam - ch_dedup = BWAMETH.out.dedup - ch_aligner_mqc = BWAMETH.out.mqc + ch_bam = FASTQ_ALIGN_DEDUP_BWAMETH.out.bam + ch_bai = FASTQ_ALIGN_DEDUP_BWAMETH.out.bai + ch_aligner_mqc = FASTQ_ALIGN_DEDUP_BWAMETH.out.multiqc + ch_versions = ch_versions.mix(FASTQ_ALIGN_DEDUP_BWAMETH.out.versions.unique{ it.baseName }) } // // MODULE: Qualimap BamQC + // skipped by default. to use run with `--run_qualimap` param. // - QUALIMAP_BAMQC ( - ch_dedup, - params.bamqc_regions_file ? Channel.fromPath( params.bamqc_regions_file, checkIfExists: true ).toList() : [] - ) - ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first()) + if(params.run_qualimap) { + QUALIMAP_BAMQC ( + ch_bam, + params.bamqc_regions_file ? Channel.fromPath( params.bamqc_regions_file, checkIfExists: true ).toList() : [] + ) + ch_qualimap = QUALIMAP_BAMQC.out.results + ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first()) + } // - // MODULE: Run Preseq + // MODULE: Preseq LCEXTRAP + // skipped by default. to use run with `--run_preseq` param. // - PRESEQ_LCEXTRAP (ch_bam) - ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions.first()) + if(params.run_preseq) { + PRESEQ_LCEXTRAP ( + ch_bam + ) + ch_preseq = PRESEQ_LCEXTRAP.out.lc_extrap + ch_versions = ch_versions.mix(PRESEQ_LCEXTRAP.out.versions.first()) + } // // Collate and save software versions // - softwareVersionsToYAML(ch_versions) - .collectFile( - storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_pipeline_software_mqc_versions.yml', - sort: true, - newLine: true - ).set { ch_collated_versions } + ch_collated_versions = softwareVersionsToYAML(ch_versions) + .collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'nf_core_' + 'methylseq_software_' + 'mqc_' + 'versions.yml', + sort: true, + newLine: true + ) // // MODULE: MultiQC @@ -169,8 +191,12 @@ workflow METHYLSEQ { ) ) - ch_multiqc_files = ch_multiqc_files.mix(QUALIMAP_BAMQC.out.results.collect{ it[1] }.ifEmpty([])) - ch_multiqc_files = ch_multiqc_files.mix(PRESEQ_LCEXTRAP.out.log.collect{ it[1] }.ifEmpty([])) + if(params.run_qualimap) { + ch_multiqc_files = ch_multiqc_files.mix(QUALIMAP_BAMQC.out.results.collect{ it[1] }.ifEmpty([])) + } + if (params.run_preseq) { + ch_multiqc_files = ch_multiqc_files.mix(PRESEQ_LCEXTRAP.out.log.collect{ it[1] }.ifEmpty([])) + } ch_multiqc_files = ch_multiqc_files.mix(ch_aligner_mqc.ifEmpty([])) if (!params.skip_trimming) { ch_multiqc_files = ch_multiqc_files.mix(TRIMGALORE.out.log.collect{ it[1] }) @@ -187,7 +213,11 @@ workflow METHYLSEQ { ) emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html + bam = ch_bam // channel: [ val(meta), path(bam) ] + bai = ch_bai // channel: [ val(meta), path(bai) ] + qualimap = ch_qualimap // channel: [ val(meta), path(qualimap) ] + preseq = ch_preseq // channel: [ val(meta), path(preseq) ] + multiqc_report = MULTIQC.out.report.toList() // channel: [ path(multiqc_report.html ) ] versions = ch_versions // channel: [ path(versions.yml) ] } diff --git a/workflows/methylseq/nextflow.config b/workflows/methylseq/nextflow.config index e1ee85ad..848b3085 100644 --- a/workflows/methylseq/nextflow.config +++ b/workflows/methylseq/nextflow.config @@ -1,13 +1,14 @@ +// module configs +includeConfig "../../conf/modules/fastqc.config" +includeConfig "../../conf/modules/trimgalore.config" +includeConfig "../../conf/modules/multiqc.config" +includeConfig "../../conf/modules/preseq_lcextrap.config" +includeConfig "../../conf/modules/qualimap_bamqc.config" -includeConfig "../../subworkflows/local/bismark/nextflow.config" -includeConfig "../../subworkflows/local/bwameth/nextflow.config" -includeConfig "../../subworkflows/local/prepare_genome/nextflow.config" - -includeConfig "../../modules/nf-core/fastqc/nextflow.config" -includeConfig "../../modules/nf-core/trimgalore/nextflow.config" -includeConfig "../../modules/nf-core/multiqc/nextflow.config" -includeConfig "../../modules/nf-core/preseq/lcextrap/nextflow.config" -includeConfig "../../modules/nf-core/qualimap/bamqc/nextflow.config" +// subworkflow configs +includeConfig "../../conf/subworkflows/fasta_index_bismark_bwameth.config" +includeConfig "../../conf/subworkflows/fastq_align_dedup_bismark.config" +includeConfig "../../conf/subworkflows/fastq_align_dedup_bwameth.config" process {