diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index e316f2a6..b0818696 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -19,7 +19,7 @@ If you'd like to write some code for nf-core/airrflow, the standard workflow is 1. Check that there isn't already an issue about your idea in the [nf-core/airrflow issues](https://github.com/nf-core/airrflow/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/airrflow repository](https://github.com/nf-core/airrflow) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) -4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). +4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). @@ -40,7 +40,7 @@ There are typically two types of tests that run: ### Lint tests `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. -To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. +To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core pipelines lint ` command. If any failures or warnings are encountered, please follow the listed URL for more documentation. @@ -75,7 +75,7 @@ If you wish to contribute a new step, please use the following coding standards: 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). -5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). +5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core pipelines schema build` tool). 6. Add sanity checks and validation for all relevant parameters. 7. Perform local tests to validate that the new code works as expected. 8. If applicable, add a new test command in `.github/workflow/ci.yml`. @@ -86,11 +86,11 @@ If you wish to contribute a new step, please use the following coding standards: Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. -Once there, use `nf-core schema build` to add to `nextflow_schema.json`. +Once there, use `nf-core pipelines schema build` to add to `nextflow_schema.json`. ### Default processes resource requirements -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block. @@ -103,7 +103,7 @@ Please use the following naming schemes, to make it easy to understand what is g ### Nextflow version bumping -If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` +If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` ### Images and figures diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 1c3a0658..10c78756 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -17,7 +17,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/airr - [ ] If you've fixed a bug or added code that should be tested, add tests! - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/airrflow/tree/master/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/airrflow _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. -- [ ] Make sure your code lints (`nf-core lint`). +- [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 9c799e4b..9f62bde3 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -1,18 +1,35 @@ name: nf-core AWS full size tests -# This workflow is triggered on published releases. +# This workflow is triggered on PRs opened against the master branch. # It can be additionally triggered manually with GitHub actions workflow dispatch button. # It runs the -profile 'test_full' on AWS batch on: - release: - types: [published] + pull_request: + branches: + - master workflow_dispatch: + pull_request_review: + types: [submitted] + jobs: run-platform: name: Run AWS full tests - if: github.repository == 'nf-core/airrflow' + # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered + if: github.repository == 'nf-core/airrflow' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch' runs-on: ubuntu-latest steps: + - uses: octokit/request-action@v2.x + id: check_approvals + with: + route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + - id: test_variables + if: github.event_name != 'workflow_dispatch' + run: | + JSON_RESPONSE='${{ 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/ci.yml b/.github/workflows/ci.yml index e3ff5e02..015a1439 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -7,9 +7,14 @@ on: pull_request: release: types: [published] + workflow_dispatch: env: NXF_ANSI_LOG: false + NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity + NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity + ACTIONS_RUNNER_DEBUG: true + ACTIONS_STEP_DEBUG: true concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" @@ -17,30 +22,68 @@ concurrency: jobs: test: - name: Run pipeline with test data + name: "Run pipeline with test data (${{ 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/airrflow') }} runs-on: ubuntu-latest strategy: matrix: NXF_VER: - - "23.04.0" + - "24.04.2" - "latest-everything" + profile: + - "docker" + - "singularity" + test_name: + - "test" + isMaster: + - ${{ github.base_ref == 'master' }} + # Exclude conda and singularity on dev + exclude: + - isMaster: false + profile: "conda" + - isMaster: false + profile: "singularity" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Install Nextflow + - name: Set up Nextflow uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" - - name: Disk space cleanup + - 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 pipeline with test data + - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}" run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results test_profile: name: Run workflow test with different profiles @@ -49,7 +92,7 @@ jobs: strategy: matrix: NXF_VER: - - "23.04.0" + - "24.04.2" - "latest-everything" profile: [ @@ -62,14 +105,18 @@ jobs: "test_10x_sc", "test_clontech_umi", "test_nebnext_umi", + "test_rnaseq_bulk", + "test_rnaseq_sc", + "test_maskprimers_extract", + "test_maskprimers_align", ] fail-fast: false steps: - name: Check out pipeline code - uses: actions/checkout@v3 + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" @@ -79,7 +126,7 @@ jobs: - name: Upload logs on failure if: failure() - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v4 with: name: logs-${{ matrix.profile }} path: | diff --git a/.github/workflows/ci_immcantation.yml b/.github/workflows/ci_immcantation.yml index 9301f01a..04162975 100644 --- a/.github/workflows/ci_immcantation.yml +++ b/.github/workflows/ci_immcantation.yml @@ -20,7 +20,7 @@ jobs: strategy: matrix: NXF_VER: - - "23.04.0" + - "24.04.2" - "latest-everything" profile: [ @@ -34,7 +34,7 @@ jobs: uses: actions/checkout@v3 - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 + uses: nf-core/setup-nextflow@v2 with: version: "${{ matrix.NXF_VER }}" @@ -44,7 +44,7 @@ jobs: - name: Upload logs on failure if: failure() - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v4 with: name: logs-${{ matrix.profile }} path: | diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2d20d644..713dc3e7 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -1,4 +1,4 @@ -name: Test successful pipeline download with 'nf-core download' +name: Test successful pipeline download with 'nf-core pipelines download' # Run the workflow when: # - dispatched manually @@ -8,7 +8,7 @@ on: workflow_dispatch: inputs: testbranch: - description: "The specific branch you wish to utilize for the test execution of nf-core download." + description: "The specific branch you wish to utilize for the test execution of nf-core pipelines download." required: true default: "dev" pull_request: @@ -39,9 +39,11 @@ jobs: with: python-version: "3.12" architecture: "x64" - - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7 + + - name: Setup Apptainer + uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0 with: - singularity-version: 3.8.3 + apptainer-version: 1.3.4 - name: Install dependencies run: | @@ -54,33 +56,64 @@ jobs: echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + - name: Make a cache directory for the container images + run: | + mkdir -p ./singularity_container_images + - name: Download the pipeline env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core download ${{ env.REPO_LOWERCASE }} \ + nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ --revision ${{ env.REPO_BRANCH }} \ --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ - --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ + --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io" \ --container-cache-utilisation 'amend' \ - --download-configuration + --download-configuration 'yes' - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }} + - name: Count the downloaded number of container images + id: count_initial + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Initial container image count: $image_count" + echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + - name: Run the downloaded pipeline (stub) id: stub_run_pipeline continue-on-error: true env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline if: ${{ job.steps.stub_run_pipeline.status == failure() }} env: - NXF_SINGULARITY_CACHEDIR: ./ + NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + + - name: Count the downloaded number of container images + id: count_afterwards + run: | + image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) + echo "Post-pipeline run container image count: $image_count" + echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + + - name: Compare container image counts + run: | + if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ env.IMAGE_COUNT_INITIAL }} + final_count=${{ env.IMAGE_COUNT_AFTER }} + difference=$((final_count - initial_count)) + echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" + tree ./singularity_container_images + exit 1 + else + echo "The pipeline can be downloaded successfully!" + fi diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 1fcafe88..a502573c 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,6 +1,6 @@ name: nf-core linting # This workflow is triggered on pushes and PRs to the repository. -# It runs the `nf-core lint` and markdown lint tests to ensure +# It runs the `nf-core pipelines lint` and markdown lint tests to ensure # that the code meets the nf-core guidelines. on: push: @@ -41,17 +41,32 @@ jobs: python-version: "3.12" architecture: "x64" + - name: read .nf-core.yml + uses: pietrobolcato/action-read-yaml@1.1.0 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + - name: Install dependencies run: | python -m pip install --upgrade pip - pip install nf-core + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Run nf-core pipelines lint + if: ${{ github.base_ref != 'master' }} + env: + GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} + run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - - name: Run nf-core lint + - name: Run nf-core pipelines lint --release + if: ${{ github.base_ref == 'master' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} - run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md + run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md - name: Save PR number if: ${{ always() }} diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml index 40acc23f..42e519bf 100644 --- a/.github/workflows/linting_comment.yml +++ b/.github/workflows/linting_comment.yml @@ -11,7 +11,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Download lint results - uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3 + uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6 with: workflow: linting.yml workflow_conclusion: completed diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml index 03ecfcf7..c6ba35df 100644 --- a/.github/workflows/release-announcements.yml +++ b/.github/workflows/release-announcements.yml @@ -12,7 +12,7 @@ jobs: - name: get topics and convert to hashtags id: get_topics run: | - echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT + echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" | sed 's/-//g' >> $GITHUB_OUTPUT - uses: rzr/fediverse-action@master with: diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml new file mode 100644 index 00000000..e8aafe44 --- /dev/null +++ b/.github/workflows/template_version_comment.yml @@ -0,0 +1,46 @@ +name: nf-core template version comment +# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version. +# It posts a comment to the PR, even if it comes from a fork. + +on: pull_request_target + +jobs: + template_version: + runs-on: ubuntu-latest + steps: + - name: Check out pipeline code + uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 + with: + ref: ${{ github.event.pull_request.head.sha }} + + - name: Read template version from .nf-core.yml + uses: nichmor/minimal-read-yaml@v0.0.2 + id: read_yml + with: + config: ${{ github.workspace }}/.nf-core.yml + + - name: Install nf-core + run: | + python -m pip install --upgrade pip + pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} + + - name: Check nf-core outdated + id: nf_core_outdated + run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV} + + - name: Post nf-core template version comment + uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2 + if: | + contains(env.OUTPUT, 'nf-core') + with: + repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }} + allow-repeats: false + message: | + > [!WARNING] + > Newer version of the nf-core template is available. + > + > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}. + > Please update your pipeline to the latest version. + > + > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync). + # diff --git a/.gitignore b/.gitignore index 9f348012..a42ce016 100644 --- a/.gitignore +++ b/.gitignore @@ -6,10 +6,4 @@ results/ testing/ testing* *.pyc -node_modules/ -package-lock.json -.idea/ -nf-params.json -.vscode/ -tests/ -test_flow/ +null/ diff --git a/.gitpod.yml b/.gitpod.yml index 105a1821..46118637 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,17 +4,14 @@ tasks: command: | pre-commit install --install-hooks nextflow self-update - - name: unset JAVA_TOOL_OPTIONS - command: | - 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 + #- 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 + - 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 diff --git a/.nf-core.yml b/.nf-core.yml index da47f3f0..159deec3 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,3 +1,4 @@ +bump_version: null lint: files_exist: - conf/igenomes.config @@ -11,5 +12,18 @@ lint: - params.report_logo - params.report_logo_img - params.config_profile_url + included_configs: False +nf_core_version: 3.0.2 +org_path: null repository_type: pipeline -nf_core_version: "2.14.1" +template: + author: Gisela Gabernet, Susanna Marquez, Alexander Peltzer, Simon Heumos + description: B and T cell repertoire analysis pipeline with the Immcantation framework. + force: false + is_nfcore: true + name: airrflow + org: nf-core + outdir: . + skip_features: null + version: 4.1.0 +update: null diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4dc0f1dc..9e9f0e1c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,7 +7,7 @@ repos: - prettier@3.2.5 - repo: https://github.com/editorconfig-checker/editorconfig-checker.python - rev: "2.7.3" + rev: "3.0.3" hooks: - id: editorconfig-checker alias: ec diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 00000000..cee7b74a --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,6 @@ +{ + "[python]": { + "editor.defaultFormatter": "ms-python.black-formatter" + }, + "python.formatting.provider": "none" +} diff --git a/CHANGELOG.md b/CHANGELOG.md index a9cf4c5e..f63d8f7a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,38 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). -## [4.1.0] - +## [4.2.0] - Evanesco + +### `Added` + +- [#334](https://github.com/nf-core/airrflow/pull/334) Added TRUST4 support. +- [#344](https://github.com/nf-core/airrflow/pull/344) Added option to remove V and C primer region when sequence is unknown. +- [#344](https://github.com/nf-core/airrflow/pull/344) Added option to save non-productive sequences +- [#344](https://github.com/nf-core/airrflow/pull/344) Allow for maskprimers align with UMI on both V gene and C gene primers. +- [#344](https://github.com/nf-core/airrflow/pull/344) Update pipeline template to nf-core tools v3.0.2. +- [357](https://github.com/nf-core/airrflow/pull/357) Deprecate isotype_column parameter in favor of annotating C region from internal c_region alignment or c_primer alignment into the c_call column. + +### `Fixed` + +- [#344](https://github.com/nf-core/airrflow/pull/344) Avoid saving pRESTO intermediate fastq files in results directory. +- [#344](https://github.com/nf-core/airrflow/pull/344) Simplified pRESTO Maskprimers score and Maskprimers extract processes. +- [#344](https://github.com/nf-core/airrflow/pull/344) Fix clustersets approach, consider both reads clusters annotation. +- [#344](https://github.com/nf-core/airrflow/pull/344) Allow for partial alignments in MakeDB for mouse TCR data, to bypass junction check for TRAV germlines with additional positions (e.g. 84A). +- [#344](https://github.com/nf-core/airrflow/pull/344) Fix parse logs merging dataframes using pandas join to produce logs even when there are failing samples. +- [#344](https://github.com/nf-core/airrflow/pull/344) Use pRESTO Collapseseq with n=0 by default due to runtime issues. + +### `Dependencies` + +| Dependency | Old version | New version | +| ---------- | ----------- | ----------- | +| enchantr | 0.1.16 | 0.1.19 | +| presto | 0.7.1 | 0.7.2 | + +### `Deprecated parameters` + +- `isotype_column`: if `c_call` column value is NA, now `c_region` and `c_primer` column values respectively are annotated into the `c_call` column. + +## [4.1.0] - Avenseguim ### `Added` diff --git a/CITATIONS.md b/CITATIONS.md index 4300d353..2c952cc7 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -4,7 +4,7 @@ > **nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework** > -> Gisela Gabernet, Susanna Marquez, Robert Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Y. Lee, Cole Jensen, David Ladd, Friederike Hanssen, Simon Heumos, nf-core community, Gur Yaari, Markus C. Kowarik, Sven Nahnsen, Steven H. Kleinstein. BioRxiv. 2024. doi: [10.1101/2024.01.18.576147](https://doi.org/10.1101/2024.01.18.576147). +> Gisela Gabernet, Susanna Marquez, Robert Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Y. Lee, Cole G. Jensen, David Ladd, Mark Polster, Friederike Hanssen, Simon Heumos, nf-core community, Gur Yaari, Markus C. Kowarik, Sven Nahnsen, Steven H. Kleinstein. (2024) PLOS Computational Biology, 20(7), e1012265. doi: [https://doi.org/10.1371/journal.pcbi.1012265](https://doi.org/10.1371/journal.pcbi.1012265). Pubmed PMID: 39058741. ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) @@ -18,7 +18,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - [Fastp](https://doi.org/10.1093/bioinformatics/bty560) @@ -62,7 +62,7 @@ - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. ## Software packaging/containerisation tools diff --git a/LICENSE b/LICENSE index 2a949fd4..206fa6b6 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) Gisela Gabernet, Susanna Marquez, Alexander Peltzer, Simon Heumos +Copyright (c) Gisela Gabernet, Susanna Marquez, Alexander Peltzer Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 28a2428b..93d8d057 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,8 @@ [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/airrflow/results) [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.2642009-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.2642009) [![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%A523.04.0-23aa62.svg)](https://www.nextflow.io/) + +[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.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/) @@ -180,13 +181,14 @@ nf-core/airrflow was originally written by: - [Gisela Gabernet](https://github.com/ggabernet) - [Susanna Marquez](https://github.com/ssnn-airr) -- [Alexander Peltzer](@apeltzer) -- [Simon Heumos](@subwaystation) +- [Alexander Peltzer](https://github.com/apeltzer) We thank the following people for their extensive assistance in the development of the pipeline: - [David Ladd](https://github.com/dladd) -- [Friederike Hanssen](https://github.com/ggabernet/friederikehanssen) +- [Friederike Hanssen](https://github.com/friederikehanssen) +- [Simon Heumos](https://github.com/subwaystation) +- [Mark Polster](https://github.com/mapo9) ## Contributions and Support @@ -196,13 +198,11 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations -If you use nf-core/airrflow for your analysis, please cite the preprint as follows: +If you use nf-core/airrflow for your analysis, please cite the article as follows: > **nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework** > -> Gisela Gabernet, Susanna Marquez, Robert Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Y. Lee, Cole Jensen, David Ladd, Friederike Hanssen, Simon Heumos, nf-core community, Gur Yaari, Markus C. Kowarik, Sven Nahnsen, Steven H. Kleinstein. -> -> BioRxiv. 2024. doi: [10.1101/2024.01.18.576147](https://doi.org/10.1101/2024.01.18.576147). +> Gisela Gabernet, Susanna Marquez, Robert Bjornson, Alexander Peltzer, Hailong Meng, Edel Aron, Noah Y. Lee, Cole G. Jensen, David Ladd, Mark Polster, Friederike Hanssen, Simon Heumos, nf-core community, Gur Yaari, Markus C. Kowarik, Sven Nahnsen, Steven H. Kleinstein. (2024) PLOS Computational Biology, 20(7), e1012265. doi: [https://doi.org/10.1371/journal.pcbi.1012265](https://doi.org/10.1371/journal.pcbi.1012265). Pubmed PMID: 39058741. The specific pipeline version using the following DOI: [10.5281/zenodo.2642009](https://doi.org/10.5281/zenodo.2642009) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 23dcd315..8adc84c9 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,8 @@ report_comment: > - This report has been generated by the nf-core/airrflow + + This report has been generated by the nf-core/airrflow analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. module_order: - fastqc: diff --git a/assets/repertoire_comparison.Rmd b/assets/repertoire_comparison.Rmd index b16a9cf4..70225fda 100644 --- a/assets/repertoire_comparison.Rmd +++ b/assets/repertoire_comparison.Rmd @@ -74,13 +74,13 @@ tryCatch( { write.table(tab_seqs, file=paste0(seq_dir,"/Table_sequences_assembly.tsv"), sep="\t", quote=F, row.names=F) plot_table <- tidyr::pivot_longer(tab_seqs, - cols=Sequences_R1:Igblast, + cols=Sequences:Igblast, names_to = "steps", values_to ="count") - plot_table$steps <- factor(plot_table$steps, levels=c("Sequences_R1", "Sequences_R2", "Filtered_quality_R1", - "Filtered_quality_R2", "Mask_primers_R1", "Mask_primers_R2", - "Paired", "Build_consensus", "Assemble_pairs", "Unique", - "Representative_2", "Igblast")) + firstcol = which(colnames(tab_seqs) == "Sequences") + lastcol = which(colnames(tab_seqs) == "Igblast") + plot_table$steps <- factor(plot_table$steps, levels=colnames(tab_seqs)[firstcol:lastcol]) + seqs_plot <- ggplot(data=plot_table, aes(x=steps, y=count, group=sample_id)) + geom_line(aes(colour=sample_id)) + diff --git a/assets/schema_input.json b/assets/schema_input.json index bb0ee0ba..686f8ef7 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/airrflow/master/assets/schema_input.json", "title": "nf-core/airrflow pipeline - params.input schema", "description": "Schema for the file provided with params.input", @@ -37,7 +37,7 @@ "errorMessage": "Sex must be provided, specify NA if unknown." }, "age": { - "type": "string", + "type": ["string", "integer"], "errorMessage": "Age must be provided, specify NA if unknown." }, "biomaterial_provider": { @@ -48,6 +48,26 @@ "type": "boolean", "pattern": "^\\S+$", "errorMessage": "Single cell must be provided as a TRUE/FALSE value." + }, + "filename_R1": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Filename for R1 cannot contain spaces." + }, + "filename_R2": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Filename for R2 cannot contain spaces." + }, + "filename_I1": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Filename for I1 cannot contain spaces." + }, + "filename": { + "type": "string", + "pattern": "^\\S+$", + "errorMessage": "Filename cannot contain spaces." } }, "required": [ diff --git a/assets/tutorial/airrflow.sh b/assets/tutorial/airrflow.sh index 34022df7..97fcf1e1 100644 --- a/assets/tutorial/airrflow.sh +++ b/assets/tutorial/airrflow.sh @@ -1,9 +1,7 @@ -nextflow run nf-core/airrflow -r 4.1.0 \ +nextflow run nf-core/airrflow -r 4.2.0 \ -profile docker \ --mode assembled \ --input samplesheet.tsv \ --outdir results \ -w work \ ---max_cpus 12 \ ---max_memory 12.GB \ --skip_multiqc diff --git a/bin/log_parsing.py b/bin/log_parsing.py index d262f51b..554c7d05 100755 --- a/bin/log_parsing.py +++ b/bin/log_parsing.py @@ -244,7 +244,7 @@ with open(logfile, "r") as f: for line in f: if "PASS>" in line: - s_code.append(logfile.split("/")[1].split("_command_log")[0]) + s_code.append(logfile.split("/")[1].split("_makedb_command_log")[0]) pass_blast.append(line.strip().removeprefix("PASS> ")) elif "FAIL>" in line: fail_blast.append(line.strip().removeprefix("FAIL> ")) @@ -368,9 +368,7 @@ # Getting table colnames colnames = [ - "Sample", - "Sequences_R1", - "Sequences_R2", + "Sequences", "Filtered_quality_R1", "Filtered_quality_R2", "Mask_primers_R1", @@ -386,24 +384,24 @@ print(df_process_list[0].sort_values(by=["Sample"]).pivot(index="Sample", columns="readtype")) values = [ - df_process_list[2].sort_values(by=["Sample"]).iloc[:, 0].tolist(), - df_process_list[0].sort_values(by=["Sample"]).pivot(index="Sample", columns="readtype")["start"]["R1"].tolist(), - df_process_list[0].sort_values(by=["Sample"]).pivot(index="Sample", columns="readtype")["start"]["R2"].tolist(), - df_process_list[0].sort_values(by=["Sample"]).pivot(index="Sample", columns="readtype")["pass"]["R1"].tolist(), - df_process_list[0].sort_values(by=["Sample"]).pivot(index="Sample", columns="readtype")["pass"]["R2"].tolist(), - df_process_list[1].sort_values(by=["Sample"]).pivot(index="Sample", columns="readtype")["pass"]["R1"].tolist(), - df_process_list[1].sort_values(by=["Sample"]).pivot(index="Sample", columns="readtype")["pass"]["R2"].tolist(), - df_process_list[2].sort_values(by=["Sample"]).loc[:, "pass_pairs"].tolist(), - df_process_list[4].sort_values(by=["Sample"]).loc[:, "pass_pairs"].tolist(), - df_process_list[5].sort_values(by=["Sample"]).loc[:, "pass_pairs"].tolist(), - df_process_list[6].sort_values(by=["Sample"]).loc[:, "unique"].tolist(), - df_process_list[7].sort_values(by=["Sample"]).loc[:, "repres_2"].tolist(), - df_process_list[7].sort_values(by=["Sample"]).loc[:, "pass_igblast"].tolist(), + df_process_list[0].pivot(index="Sample", columns="readtype")["start"]["R1"], + df_process_list[0].pivot(index="Sample", columns="readtype")["pass"]["R1"], + df_process_list[0].pivot(index="Sample", columns="readtype")["pass"]["R2"], + df_process_list[1].pivot(index="Sample", columns="readtype")["pass"]["R1"], + df_process_list[1].pivot(index="Sample", columns="readtype")["pass"]["R2"], + df_process_list[2].set_index("Sample").loc[:, "pass_pairs"], + df_process_list[4].set_index("Sample").loc[:, "pass_pairs"], + df_process_list[5].set_index("Sample").loc[:, "pass_pairs"], + df_process_list[6].set_index("Sample").loc[:, "unique"], + df_process_list[7].set_index("Sample").loc[:, "repres_2"], + df_process_list[7].set_index("Sample").loc[:, "pass_igblast"], ] +final_table = pd.concat(values, axis=1, join="outer") +final_table.columns = colnames +final_table = final_table.reset_index().rename(columns={"index": "Sample"}) + -final_table = dict(zip(colnames, values)) -print(final_table) df_final_table = pd.DataFrame.from_dict(final_table) df_final_table = df_final_table.sort_values(["Sample"], ascending=[1]) diff --git a/bin/log_parsing_no-umi.py b/bin/log_parsing_no-umi.py index 98367764..417a1367 100755 --- a/bin/log_parsing_no-umi.py +++ b/bin/log_parsing_no-umi.py @@ -1,5 +1,5 @@ #!/usr/bin/env python3 -# Written by David Ladd and released under the MIT license (2020). +# Written by David Ladd, Gisela Gabernet and released under the MIT license (2020). # log_parsing_no-umi.py # Parsing log files for each of the steps for QC analysis. @@ -23,7 +23,7 @@ df_process_list = [] for process in processes: - find = subprocess.check_output(["find", process, "-name", "*command_log.txt"]) + find = subprocess.check_output(["find", process, "-name", "*command_log*"]) log_files = find.decode().split("\n") log_files = list(filter(None, log_files)) @@ -59,49 +59,67 @@ df_process_list.append(df_process) - elif process in ["mask_primers", "filter_by_sequence_quality"]: + if process in ["filter_by_sequence_quality"]: s_code = [] + pass_pairs = [] + fail_pairs = [] + process_name = [] + + for logfile in log_files: + with open(logfile, "r") as f: + for line in f: + if " START>" in line: + s_code.append(logfile.split("/")[1].split("_command_log")[0]) + process_name.append(process) + elif "PASS>" in line: + pass_pairs.append(line.strip().removeprefix("PASS> ")) + elif "FAIL>" in line: + fail_pairs.append(line.strip().removeprefix("FAIL> ")) + + df_process = pd.DataFrame.from_dict( + { + "Sample": s_code, + "pass_pairs": pass_pairs, + "fail_pairs": fail_pairs, + "process": process_name, + } + ) + + df_process_list.append(df_process) + + elif process in ["mask_primers"]: + s_code = [] + s_readtype = [] output_file = [] - seqs_R1 = [] - seqs_R2 = [] - pass_R1 = [] - pass_R2 = [] - fail_R1 = [] - fail_R2 = [] + n_seqs = [] + n_pass = [] + n_fail = [] process_name = [] for logfile in log_files: - c = 0 + if "_R1" in logfile: + s_readtype.append("R1") + elif "_R2" in logfile: + s_readtype.append("R2") with open(logfile, "r") as f: - # print(f.read()) for line in f: if " START>" in line: - if c < 1: - s_code.append(logfile.split("/")[1].split("_command_log")[0]) - process_name.append(process) + s_code.append(logfile.split("/")[1].split("_command_log")[0]) + process_name.append(process) elif "SEQUENCES>" in line: - if c < 1: - seqs_R1.append(line.strip().removeprefix("SEQUENCES> ")) - else: - seqs_R2.append(line.strip().removeprefix("SEQUENCES> ")) + n_seqs.append(line.strip().removeprefix("SEQUENCES> ")) elif "PASS>" in line: - if c < 1: - pass_R1.append(line.strip().removeprefix("PASS> ")) - else: - pass_R2.append(line.strip().removeprefix("PASS> ")) + n_pass.append(line.strip().removeprefix("PASS> ")) elif "FAIL>" in line: - if c < 1: - fail_R1.append(line.strip().removeprefix("FAIL> ")) - c += 1 - else: - fail_R2.append(line.strip().removeprefix("FAIL> ")) + n_fail.append(line.strip().removeprefix("FAIL> ")) df_process = pd.DataFrame.from_dict( { "Sample": s_code, - "start_R1": seqs_R1, - "pass_R1": pass_R1, - "fail_R1": fail_R1, + "readtype": s_readtype, + "start": n_seqs, + "pass": n_pass, + "fail": n_fail, "process": process_name, } ) @@ -282,23 +300,13 @@ "Sequences", "Assemble_pairs", "Filtered_quality", - "Mask_primers", + "Mask_primers_R1", + "Mask_primers_R2", "Unique", "Representative_2", "Igblast", ] -values = [ - df_process_list[0].sort_values(by=["Sample"]).iloc[:, 0].tolist(), - df_process_list[0].sort_values(by=["Sample"]).loc[:, "start_pairs"].tolist(), - df_process_list[0].sort_values(by=["Sample"]).loc[:, "pass_pairs"].tolist(), - df_process_list[1].sort_values(by=["Sample"]).loc[:, "pass_R1"].tolist(), - df_process_list[2].sort_values(by=["Sample"]).loc[:, "pass_R1"].tolist(), - df_process_list[3].sort_values(by=["Sample"]).loc[:, "unique"].tolist(), - df_process_list[4].sort_values(by=["Sample"]).loc[:, "repres_2"].tolist(), - df_process_list[4].sort_values(by=["Sample"]).loc[:, "pass_igblast"].tolist(), -] - # Tables provide extra info and help debugging df_process_list[0].to_csv( path_or_buf="Table_all_details_assemble_mates.tsv", @@ -316,6 +324,18 @@ df_process_list[3].to_csv(path_or_buf="Table_all_details_deduplicate.tsv", sep="\t", header=True, index=False) df_process_list[4].to_csv(path_or_buf="Table_all_details_igblast.tsv", sep="\t", header=True, index=False) +values = [ + df_process_list[0].sort_values(by=["Sample"]).iloc[:, 0].tolist(), + df_process_list[0].sort_values(by=["Sample"]).loc[:, "start_pairs"].tolist(), + df_process_list[0].sort_values(by=["Sample"]).loc[:, "pass_pairs"].tolist(), + df_process_list[1].sort_values(by=["Sample"]).loc[:, "pass_pairs"].tolist(), + df_process_list[2].sort_values(by=["Sample"]).pivot(index="Sample", columns="readtype")["pass"]["R1"].tolist(), + df_process_list[2].sort_values(by=["Sample"]).pivot(index="Sample", columns="readtype")["pass"]["R2"].tolist(), + df_process_list[3].sort_values(by=["Sample"]).loc[:, "unique"].tolist(), + df_process_list[4].sort_values(by=["Sample"]).loc[:, "repres_2"].tolist(), + df_process_list[4].sort_values(by=["Sample"]).loc[:, "pass_igblast"].tolist(), +] + final_table = dict(zip(colnames, values)) print(final_table) df_final_table = pd.DataFrame.from_dict(final_table) diff --git a/conf/base.config b/conf/base.config index 6606bdac..9d512264 100644 --- a/conf/base.config +++ b/conf/base.config @@ -9,9 +9,10 @@ */ process { - cpus = { check_max( 1 * task.attempt, 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + + cpus = { 1 * task.attempt } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 @@ -24,30 +25,30 @@ process { // adding in your local modules too. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { - cpus = { check_max( 1 , 'cpus' ) } - memory = { check_max( 6.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 1 } + memory = { 6.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_low { - cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 12.GB * task.attempt, 'memory' ) } - time = { check_max( 4.h * task.attempt, 'time' ) } + cpus = { 2 * task.attempt } + memory = { 12.GB * task.attempt } + time = { 4.h * task.attempt } } withLabel:process_medium { - cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } - time = { check_max( 8.h * task.attempt, 'time' ) } + cpus = { 6 * task.attempt } + memory = { 36.GB * task.attempt } + time = { 8.h * task.attempt } } withLabel:process_high { - cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } - time = { check_max( 16.h * task.attempt, 'time' ) } + cpus = { 12 * task.attempt } + memory = { 72.GB * task.attempt } + time = { 16.h * task.attempt } } withLabel:process_long { - time = { check_max( 20.h * task.attempt, 'time' ) } + time = { 20.h * task.attempt } } withLabel:process_high_memory { - memory = { check_max( 200.GB * task.attempt, 'memory' ) } + memory = { 200.GB * task.attempt } } withLabel:error_ignore { errorStrategy = 'ignore' @@ -57,8 +58,8 @@ process { maxRetries = 2 } withLabel:process_long_parallelized { - time = { check_max( 30.h * task.attempt, 'time' ) } - cpus = { check_max( 16 * task.attempt, 'cpus' ) } - memory = { check_max( 72.GB * task.attempt, 'memory' ) } + time = { 30.h * task.attempt } + cpus = { 16 * task.attempt } + memory = { 72.GB * task.attempt } } } diff --git a/conf/clontech_umi_bcr.config b/conf/clontech_umi_bcr.config index d2d17e01..9433db7a 100644 --- a/conf/clontech_umi_bcr.config +++ b/conf/clontech_umi_bcr.config @@ -30,12 +30,12 @@ params { // Mask primer options - maskprimers_align = true - primer_extract_len = 7 - primer_mask_mode = 'cut' + maskprimers_align_race = true + primer_r2_extract_len = 7 + primer_r1_mask_mode = 'cut' + primer_r2_mask_mode = 'cut' primer_maxlen = 70 primer_r1_maxerror = 0.2 assemblepairs_sequential = true primer_consensus = 0.6 - isotype_column = 'cregion' } diff --git a/conf/clontech_umi_tcr.config b/conf/clontech_umi_tcr.config index 34aad8ab..d6b71d28 100644 --- a/conf/clontech_umi_tcr.config +++ b/conf/clontech_umi_tcr.config @@ -30,9 +30,10 @@ params { // Mask primer options - maskprimers_align = true - primer_extract_len = 7 - primer_mask_mode = 'cut' + maskprimers_align_race = true + primer_r2_extract_len = 7 + primer_r1_mask_mode = 'cut' + primer_r2_mask_mode = 'cut' primer_maxlen = 70 primer_r1_maxerror = 0.2 assemblepairs_sequential = true diff --git a/conf/igenomes_ignored.config b/conf/igenomes_ignored.config new file mode 100644 index 00000000..b4034d82 --- /dev/null +++ b/conf/igenomes_ignored.config @@ -0,0 +1,9 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for iGenomes paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Empty genomes dictionary to use when igenomes is ignored. +---------------------------------------------------------------------------------------- +*/ + +params.genomes = [:] diff --git a/conf/modules.config b/conf/modules.config index 3dc63fa9..c947dfce 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -54,7 +54,7 @@ process { ext.args = [ "--disable_quality_filtering --disable_length_filtering", params.trim_fastq ?: "--disable_adapter_trimming", params.clip_r1 > 0 ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1 - params.clip_r2 > 0 ? "--trim_front2 ${params.clip_r2}" : "", // Remove bp from the 5' end of read 2 + params.clip_r2 > 0 ? "--trim_front2 ${params.clip_r2}" : "", // Remove bp from the 5' end of read 2 params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed params.three_prime_clip_r2 > 0 ? "--trim_tail2 ${params.three_prime_clip_r2}" : "", // Remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed params.trim_nextseq ? "--trim_poly_g" : "", // Apply the --nextseq=X option, to trim based on quality after removing poly-G tails @@ -118,7 +118,7 @@ process { publishDir = [ path: { "${params.outdir}/presto/01-filterseq/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] } @@ -126,61 +126,139 @@ process { publishDir = [ path: { "${params.outdir}/presto/02-filterseq/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] } - withName: PRESTO_MASKPRIMERS_UMI { + withName: PRESTO_MASKPRIMERS_SCORE_UMI_R1 { publishDir = [ path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] + ext.args2 = '-f ID PRIMER ERROR' } - withName: PRESTO_MASKPRIMERS_ALIGN { + withName: PRESTO_MASKPRIMERS_SCORE_UMI_R2 { publishDir = [ path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" + ] + ext.args2 = '-f ID PRIMER ERROR' + } + + withName: PRESTO_ALIGN_PRIMERS { + publishDir = [ + path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" ] - ext.args = '--skiprc --pf CREGION' - ext.args2 = '-f ID CREGION ERROR' + ext.args = '--skiprc --pf C_PRIMER' + ext.args2 = '-f ID PRIMER ERROR' } withName: PRESTO_ALIGN_CREGION { publishDir = [ path: { "${params.outdir}/presto/internal_cregion/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] - ext.args = '--skiprc --revpr --pf CREGION' + ext.args = '--skiprc --revpr --pf C_REGION' ext.args2 = '-f ID PRIMER ERROR --outname cregion_alignment' } - withName: PRESTO_MASKPRIMERS_EXTRACT { + withName: 'PRESTO_MASKPRIMERS_EXTRACT' { publishDir = [ path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" + ] + ext.args2 = '-f ID PRIMER ERROR PRSTART' + } + + withName: 'PRESTO_MASKPRIMERS_ALIGN_UMI_R1' { + publishDir = [ + path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" + ] + ext.args2 = '-f ID PRIMER ERROR PRSTART' + } + + withName: 'PRESTO_MASKPRIMERS_ALIGN_UMI_R2' { + publishDir = [ + path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" + ] + ext.args2 = '-f ID PRIMER ERROR PRSTART' + } + + withName: PRESTO_MASKPRIMERS_EXTRACT_R1 { + publishDir = [ + path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" + ] + ext.args = '--pf EXTRACT_PRIMER_R1' + ext.args2 = '-f ID PRIMER ERROR PRSTART' + } + + withName: PRESTO_MASKPRIMERS_EXTRACT_R2 { + publishDir = [ + path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" ] - ext.args = '--barcode --bf BARCODE' + ext.args = '--pf EXTRACT_PRIMER_R2' ext.args2 = '-f ID PRIMER ERROR PRSTART' } - withName: PRESTO_MASKPRIMERS_POSTASSEMBLY_SANS_UMI { + withName: PRESTO_MASKPRIMERS_SCORE_SANSUMI_FWD { publishDir = [ path: { "${params.outdir}/presto/03-maskprimers/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] + ext.args2 = '-f ID PRIMER ERROR' } + withName: PRESTO_MASKPRIMERS_SCORE_SANSUMI_REV { + publishDir = [ + path: { "${params.outdir}/presto/03-maskprimers/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" + ] + ext.args2 = '-f ID PRIMER ERROR' + } + + withName: PRESTO_MASKPRIMERS_ALIGN_SANSUMI_FWD { + publishDir = [ + path: { "${params.outdir}/presto/03-maskprimers/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" + ] + ext.args = '--pf FWD_PRIMER' + ext.args2 = '-f ID PRIMER ERROR' + } + + withName: PRESTO_MASKPRIMERS_ALIGN_SANSUMI_REV { + publishDir = [ + path: { "${params.outdir}/presto/03-maskprimers/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" + ] + ext.args = '--revpr --pf REV_PRIMER' + ext.args2 = '-f ID PRIMER ERROR' + } + + withName: PRESTO_PAIRSEQ { publishDir = [ path: { "${params.outdir}/presto/03-pairseq/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] ext.args = "--coord illumina" } @@ -189,46 +267,94 @@ process { publishDir = [ path: { "${params.outdir}/presto/03-pairseq/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" + ] + ext.args = '--1f C_REGION --coord illumina' + } + + withName: PRESTO_PAIRSEQ_EXTRACT { + publishDir = [ + path: { "${params.outdir}/presto/03-pairseq/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" ] - ext.args = '--1f CREGION --coord illumina' + ext.args = '--coord illumina' } - withName: PRESTO_CLUSTERSETS { + withName: PRESTO_CLUSTERSETS_UMI { publishDir = [ path: { "${params.outdir}/presto/04-clustersets/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] + ext.args = '--exec vsearch --ident 0.9' + ext.args2 = '-f ID BARCODE SEQCOUNT CLUSTERS' } withName: PRESTO_PARSE_CLUSTER { publishDir = [ path: { "${params.outdir}/presto/05-parse-clusters/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] } + withName: PRESTO_PAIRSEQ_CLUSTERSETS { + publishDir = [ + path: { "${params.outdir}/presto/05-parse-clusters/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" + ] + ext.args = '--coord illumina' + } + withName: PRESTO_BUILDCONSENSUS_UMI { publishDir = [ path: { "${params.outdir}/presto/06-build-consensus/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] - ext.args = '--pf PRIMER' - ext.args2 = '--pf PRIMER' + ext.args = ["--pf PRIMER --maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap}", + params.primer_consensus ? "--prcons $params.primer_consensus" : "", + params.cluster_sets ? "--bf CLUSTER" : "--bf BARCODE", + ].join(" ").trim() + ext.args2 = ["--pf PRIMER --maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap}", + params.primer_consensus ? "--prcons $params.primer_consensus" : "", + params.cluster_sets ? "--bf CLUSTER" : "--bf BARCODE", + ].join(" ").trim() ext.args3 = '-f ID BARCODE SEQCOUNT PRIMER PRCOUNT PRCONS PRFREQ CONSCOUNT ERROR' } - withName: PRESTO_BUILDCONSENSUS_ALIGN { + withName: PRESTO_BUILDCONSENSUS_ALIGN_RACE { publishDir = [ path: { "${params.outdir}/presto/06-build-consensus/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] - ext.args = '--pf CREGION' - ext.args2 = '--pf CREGION' + // Use homogeneous C_PRIMER for consensus + ext.args = ["--pf C_PRIMER --maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap}", + params.primer_consensus ? "--prcons $params.primer_consensus" : "", + params.cluster_sets ? "--bf CLUSTER" : "--bf BARCODE", + ].join(" ").trim() + // Do not use homogeneous linker for consensus + ext.args2 = ["--maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap}", + params.cluster_sets ? "--bf CLUSTER" : "--bf BARCODE", + ].join(" ").trim() + ext.args3 = '-f ID BARCODE SEQCOUNT PRIMER PRCOUNT PRCONS PRFREQ CONSCOUNT ERROR' + } + + withName: PRESTO_BUILDCONSENSUS_EXTRACT { + publishDir = [ + path: { "${params.outdir}/presto/06-build-consensus/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" + ] + ext.args = ["--maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap}", + params.cluster_sets ? "--bf CLUSTER" : "--bf BARCODE", + ].join(" ").trim() + ext.args2 = ["--maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap}", + params.cluster_sets ? "--bf CLUSTER" : "--bf BARCODE", + ].join(" ").trim() ext.args3 = '-f ID BARCODE SEQCOUNT PRIMER PRCOUNT PRCONS PRFREQ CONSCOUNT ERROR' } @@ -236,7 +362,7 @@ process { publishDir = [ path: { "${params.outdir}/presto/07-postconsensus-pairseq/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] } @@ -244,7 +370,7 @@ process { publishDir = [ path: { "${params.outdir}/presto/08-assemble-pairs/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] ext.args = '--coord presto --rc tail --1f CONSCOUNT PRCONS --2f CONSCOUNT PRCONS' ext.args2 = '-f ID BARCODE SEQCOUNT PRIMER PRCOUNT PRCONS PRFREQ CONSCOUNT LENGTH OVERLAP ERROR PVALUE' @@ -254,7 +380,7 @@ process { publishDir = [ path: { "${params.outdir}/presto/08-assemble-pairs/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] ext.args = '--coord presto --rc tail --1f CONSCOUNT --2f CONSCOUNT PRCONS --minlen 8 --maxerror 0.3 --alpha 1e-5 --scanrev --minident 0.5 --evalue 1e-5 --maxhits 100 --aligner blastn' ext.args2 = '-f ID REFID LENGTH OVERLAP GAP ERROR PVALUE EVALUE1 EVALUE2 IDENTITY FIELDS1 FIELDS2' @@ -264,9 +390,9 @@ process { publishDir = [ path: { "${params.outdir}/presto/01-assemble-pairs/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] - ext.args = '--rc tail' + ext.args = '--rc tail --coord illumina' ext.args2 = '-f ID SEQCOUNT PRIMER PRCOUNT PRFREQ LENGTH OVERLAP ERROR PVALUE' } @@ -290,7 +416,7 @@ process { enabled: false ] ext.subcommand = 'rename' - ext.args = '-f PRCONS -k CREGION' + ext.args = '-f PRCONS -k C_REGION' } withName: PRESTO_PARSEHEADERS_PRIMERS_SANS_UMI { @@ -311,9 +437,9 @@ process { publishDir = [ path: { "${params.outdir}/presto/09-collapseseq/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] - ext.args = '-n 20 --inner --uf PRCONS --cf CONSCOUNT --act sum' + ext.args = '-n 0 --inner --uf PRCONS --cf CONSCOUNT --act sum --keepmiss' ext.args2 = '-f HEADER DUPCOUNT CONSCOUNT' } @@ -321,9 +447,9 @@ process { publishDir = [ path: { "${params.outdir}/presto/09-collapseseq/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] - ext.args = '-n 0 --inner --uf CREGION --cf CONSCOUNT --act sum --keepmiss' + ext.args = '-n 0 --inner --uf C_REGION --cf CONSCOUNT --act sum --keepmiss' ext.args2 = '-f HEADER DUPCOUNT CONSCOUNT' } @@ -331,9 +457,9 @@ process { publishDir = [ path: { "${params.outdir}/presto/09-collapseseq/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] - ext.args = '-n 0 --inner --uf PRCONS CREGION --cf CONSCOUNT --act sum --keepmiss' + ext.args = '-n 0 --inner --uf PRCONS C_REGION --cf CONSCOUNT --act sum --keepmiss' ext.args2 = '-f HEADER DUPCOUNT CONSCOUNT' } @@ -341,9 +467,9 @@ process { publishDir = [ path: { "${params.outdir}/presto/04-collapseseq/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] - ext.args = '-n 20 --inner' + ext.args = '-n 0 --inner --keepmiss' ext.args2 = '-f HEADER DUPCOUNT' } @@ -351,7 +477,7 @@ process { publishDir = [ path: { "${params.outdir}/presto/10-splitseq/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] ext.args = '-f CONSCOUNT --num 2' } @@ -360,7 +486,7 @@ process { publishDir = [ path: { "${params.outdir}/presto/05-splitseq/${meta.id}" }, mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + pattern: "*{txt,log,tab}" ] ext.args = '-f DUPCOUNT --num 2' } @@ -369,7 +495,7 @@ process { // V(D)J annotation // ----------------- - withName: FETCH_DATABASES { + withName: 'FETCH_*' { publishDir = [ path: { "${params.outdir}/databases" }, mode: params.publish_dir_mode, @@ -422,6 +548,14 @@ process { ] } + withName: CHANGEO_PARSEDB_SELECT_LOCUS { + publishDir = [ + path: { "${params.outdir}/vdj_annotation/select-locus/${meta.id}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + withName: CHANGEO_PARSEDB_SPLIT { publishDir = [ path: { "${params.outdir}/vdj_annotation/04-select-productive/${meta.id}" }, diff --git a/conf/nebnext_umi_bcr.config b/conf/nebnext_umi_bcr.config index d6bb6d5b..7467bffe 100644 --- a/conf/nebnext_umi_bcr.config +++ b/conf/nebnext_umi_bcr.config @@ -35,5 +35,4 @@ params { cregion_maxlen = 100 cregion_maxerror = 0.3 cregion_mask_mode = 'tag' - isotype_column = 'cregion' } diff --git a/conf/test.config b/conf/test.config index af9618ce..642670fc 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,15 +10,18 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv' cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta' @@ -34,7 +37,6 @@ params { umi_start = 6 umi_position = 'R1' index_file = true - isotype_column = 'c_primer' lineage_trees = true } diff --git a/conf/test_10x_sc.config b/conf/test_10x_sc.config index e9b9e5a8..3fc23f69 100644 --- a/conf/test_10x_sc.config +++ b/conf/test_10x_sc.config @@ -7,15 +7,18 @@ * nextflow run nf-core/airrflow -profile test_10x_sc, */ +process { + resourceLimits = [ + cpus: 2, + memory: '6.GB', + time: '6.h' + ] +} + params { config_profile_name = 'Test 10xGenomics single cell data' config_profile_description = 'Minimal test dataset to check pipeline function with raw single cell data from 10xGenomics' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 48.h - // params mode = 'fastq' library_generation_method = 'sc_10x_genomics' diff --git a/conf/test_assembled_hs.config b/conf/test_assembled_hs.config index 9e3d7f5b..cfba51b5 100644 --- a/conf/test_assembled_hs.config +++ b/conf/test_assembled_hs.config @@ -7,15 +7,18 @@ * nextflow run nf-core/airrflow -profile test, */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test assembled mode' config_profile_description = 'Minimal test dataset to test assembled mode' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data mode = 'assembled' input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_hs.tsv' diff --git a/conf/test_assembled_immcantation_devel_hs.config b/conf/test_assembled_immcantation_devel_hs.config index c842e002..4b295024 100644 --- a/conf/test_assembled_immcantation_devel_hs.config +++ b/conf/test_assembled_immcantation_devel_hs.config @@ -7,15 +7,18 @@ * nextflow run nf-core/airrflow -profile test_assembled_immcantation_hs_devel, */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test assembled mode with Immcantation custom_container' config_profile_description = 'Minimal human test dataset to check pipeline function on assembled mode with Immcantation custom_container' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data mode = 'assembled' input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_hs.tsv' diff --git a/conf/test_assembled_immcantation_devel_mm.config b/conf/test_assembled_immcantation_devel_mm.config index e148abe8..f1eb5bfe 100644 --- a/conf/test_assembled_immcantation_devel_mm.config +++ b/conf/test_assembled_immcantation_devel_mm.config @@ -7,15 +7,18 @@ * nextflow run nf-core/airrflow -profile test_assembled_immcantation_devel_mm, */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test assembled mode with Immcantation custom_container' config_profile_description = 'Minimal mouse test dataset to check pipeline function on assembled mode with Immcantation custom_container' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data mode = 'assembled' input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_mm.tsv' diff --git a/conf/test_assembled_mm.config b/conf/test_assembled_mm.config index 43e8275e..aa65f4c1 100644 --- a/conf/test_assembled_mm.config +++ b/conf/test_assembled_mm.config @@ -7,15 +7,18 @@ * nextflow run nf-core/airrflow -profile test, */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test assembled mode' config_profile_description = 'Minimal mouse test dataset to test assembled mode' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - // Input data mode = 'assembled' input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_mm.tsv' diff --git a/conf/test_clontech_umi.config b/conf/test_clontech_umi.config index e1bf317e..cfb48f66 100644 --- a/conf/test_clontech_umi.config +++ b/conf/test_clontech_umi.config @@ -11,15 +11,18 @@ */ includeConfig 'clontech_umi_bcr.config' +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '6.h' + ] +} + params { config_profile_name = 'Test profile for TAKARA protocol' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data input = pipelines_testdata_base_path +'testdata-clontech/samplesheet.tsv' diff --git a/conf/test_fetchimgt.config b/conf/test_fetchimgt.config index 468bb52d..149bf382 100644 --- a/conf/test_fetchimgt.config +++ b/conf/test_fetchimgt.config @@ -9,16 +9,18 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} params { config_profile_name = 'Test IMGTdb fetch' config_profile_description = 'Test pipeline when fetching the latest version of the IMGT references.' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv' cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta' @@ -33,7 +35,6 @@ params { umi_start = 6 umi_position = 'R1' index_file = true - isotype_column = 'c_primer' } process{ diff --git a/conf/test_full.config b/conf/test_full.config index 9c652c8f..ac584bc5 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -9,6 +9,13 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} params { config_profile_name = 'Full test profile' @@ -29,7 +36,6 @@ params { umi_length = 15 umi_start = 0 umi_position = 'R1' - isotype_column = 'c_primer' } process { diff --git a/conf/test_maskprimers_align.config b/conf/test_maskprimers_align.config new file mode 100644 index 00000000..4c9416a1 --- /dev/null +++ b/conf/test_maskprimers_align.config @@ -0,0 +1,40 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/airrflow -profile test_maskprimers_align, --outdir + +---------------------------------------------------------------------------------------- +*/ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test maskprimers align' + config_profile_description = 'Minimal test dataset to check pipeline function' + + // Input data + input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv' + cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta' + vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' + + mode = 'fastq' + + library_generation_method = 'specific_pcr_umi' + cprimer_position = 'R1' + umi_length = 8 + umi_start = 6 + umi_position = 'R1' + index_file = true + maskprimers_align = true +} diff --git a/conf/test_maskprimers_extract.config b/conf/test_maskprimers_extract.config new file mode 100644 index 00000000..fe365915 --- /dev/null +++ b/conf/test_maskprimers_extract.config @@ -0,0 +1,51 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running minimal tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a fast and simple pipeline test. + + Use as follows: + nextflow run nf-core/airrflow -profile test, --outdir + +---------------------------------------------------------------------------------------- +*/ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test extract primers profile' + config_profile_description = 'Minimal test dataset to check pipeline function' + + // Input data + input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv' + reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip' + reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip' + + mode = 'fastq' + + library_generation_method = 'specific_pcr_umi' + maskprimers_extract = true + cprimer_position = 'R1' + umi_length = 8 + umi_start = 6 + umi_position = 'R1' + index_file = true + lineage_trees = false + primer_r1_mask_mode = 'trim' + primer_r2_mask_mode = 'cut' + primer_r1_extract_len = 28 + primer_r2_extract_len = 29 +} + +process{ + withName:"DEFINE_CLONES*"{ + ext.args = ['outname':'', 'model':'hierarchical', + 'method':'nt', 'linkage':'single', + 'outputby':'sample_id', 'min_n':10] + } +} diff --git a/conf/test_nebnext_umi.config b/conf/test_nebnext_umi.config index b26fa7cd..80e5a345 100644 --- a/conf/test_nebnext_umi.config +++ b/conf/test_nebnext_umi.config @@ -12,15 +12,18 @@ includeConfig 'nebnext_umi_bcr.config' +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { config_profile_name = 'Test profile for NEBNext protocol' config_profile_description = 'Minimal test dataset to check pipeline function' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data input = pipelines_testdata_base_path + 'testdata-neb/samplesheet.tsv' diff --git a/conf/test_no_umi.config b/conf/test_no_umi.config index 3a4fad63..19004b3b 100644 --- a/conf/test_no_umi.config +++ b/conf/test_no_umi.config @@ -6,16 +6,18 @@ * to run a fast and simple test. Use as follows: * nextflow run nf-core/airrflow -profile -c conf/test_no-umi.config */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} params { config_profile_name = 'Test profile without UMIs' config_profile_description = 'Test dataset without UMIs to check pipeline function.' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = 6.GB - max_time = 6.h - mode = 'fastq' cprimer_position = 'R1' @@ -24,7 +26,6 @@ params { vprimer_start = 4 primer_revpr = true umi_length = 0 - isotype_column = 'c_primer' // Input data input = pipelines_testdata_base_path + 'testdata-no-umi/Metadata_test-no-umi_airr.tsv' diff --git a/conf/test_nocluster.config b/conf/test_nocluster.config index 4a3fb0b7..70a11e56 100644 --- a/conf/test_nocluster.config +++ b/conf/test_nocluster.config @@ -9,16 +9,18 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} params { config_profile_name = 'Test profile no cluster sets' config_profile_description = 'Test pipeline without the cluster sets process' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv' cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta' @@ -36,7 +38,6 @@ params { cluster_sets = false index_file = true clonal_threshold = 0.15 - isotype_column = 'c_primer' } process{ diff --git a/conf/test_raw_immcantation_devel.config b/conf/test_raw_immcantation_devel.config index 567629a9..6db19108 100644 --- a/conf/test_raw_immcantation_devel.config +++ b/conf/test_raw_immcantation_devel.config @@ -9,16 +9,18 @@ ---------------------------------------------------------------------------------------- */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} params { config_profile_name = 'Test immcantation raw profile' config_profile_description = 'Minimal test dataset to check pipeline function with the immcantation container' - // Limit resources so that this can run on GitHub Actions - max_cpus = 2 - max_memory = '6.GB' - max_time = '6.h' - // Input data input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_test_airr.tsv' cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta' @@ -35,7 +37,6 @@ params { umi_start = 6 umi_position = 'R1' index_file = true - isotype_column = 'c_primer' } process{ diff --git a/conf/test_rnaseq_bulk.config b/conf/test_rnaseq_bulk.config new file mode 100644 index 00000000..a98d790c --- /dev/null +++ b/conf/test_rnaseq_bulk.config @@ -0,0 +1,28 @@ +/* + * ------------------------------------------------- + * Nextflow config file for running tests + * ------------------------------------------------- + * Defines bundled input files and everything required + * to run a fast and simple test. Use as follows: + * nextflow run nf-core/airrflow -profile test_rnaseq_bulk, + */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test bulk RNA-seq based workflow using TRUST4' + config_profile_description = 'Minimal test dataset to check pipeline function with raw bulk RNA-seq data' + + // params + mode = 'fastq' + library_generation_method = 'trust4' + clonal_threshold = 0 + + // Input data + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-rnaseq/rnaseq_metadata.tsv' +} diff --git a/conf/test_rnaseq_sc.config b/conf/test_rnaseq_sc.config new file mode 100644 index 00000000..8749a5b4 --- /dev/null +++ b/conf/test_rnaseq_sc.config @@ -0,0 +1,31 @@ +/* + * ------------------------------------------------- + * Nextflow config file for running tests + * ------------------------------------------------- + * Defines bundled input files and everything required + * to run a fast and simple test. Use as follows: + * nextflow run nf-core/airrflow -profile test_rnaseq_sc, + */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + +params { + config_profile_name = 'Test single-cell RNA-seq based workflow using TRUST4' + config_profile_description = 'Minimal test dataset to check pipeline function with raw single-cell RNA-seq data' + + // params + mode = 'fastq' + library_generation_method = 'trust4' + clonal_threshold = 0 + cell_barcode_read = "R1" + umi_read = "R1" + read_format = "bc:0:15,um:16:27" + + // Input data + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-rnaseq/sc_rnaseq_metadata.tsv' +} diff --git a/conf/test_tcr.config b/conf/test_tcr.config index 7572f099..e23871d3 100644 --- a/conf/test_tcr.config +++ b/conf/test_tcr.config @@ -7,15 +7,18 @@ * nextflow run nf-core/airrflow -profile test_tcr, */ +process { + resourceLimits = [ + cpus: 4, + memory: '15.GB', + time: '1.h' + ] +} + params { 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +ImmcantationSingle cellunselected RNA-seqCellranger FastpTRUST4Inidividual OverlapFastpvdjPostanalysis Postanalysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Repertoire and Clonotype Analysis and ReportingPDF + diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 361d0e47..00000000 Binary files a/docs/images/mqc_fastqc_adapter.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png deleted file mode 100755 index cb39ebb8..00000000 Binary files a/docs/images/mqc_fastqc_counts.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png deleted file mode 100755 index a4b89bf5..00000000 Binary files a/docs/images/mqc_fastqc_quality.png and /dev/null differ diff --git a/docs/usage.md b/docs/usage.md index c3844547..906f7910 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -41,13 +41,13 @@ nextflow run nf-core/airrflow \ A typical command to run the pipeline from **single cell raw fastq files** is: ```bash -nextflow run nf-core/airrflow -r dev \ +nextflow run nf-core/airrflow \ -profile \ --mode fastq \ --input input_samplesheet.tsv \ --library_generation_method sc_10x_genomics \ --reference_10x reference/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz \ ---outdir ./results +--outdir results ``` A typical command for running the pipeline departing from **single-cell AIRR rearrangement tables or assembled bulk sequencing fasta** data is: @@ -87,9 +87,9 @@ The above pipeline run specified with a params file in yaml format: nextflow run nf-core/airrflow -profile docker -params-file params.yaml ``` -with `params.yaml` containing: +with: -```yaml +```yaml title="params.yaml" input: './samplesheet.csv' outdir: './results/' <...> @@ -121,7 +121,7 @@ If you wish to share such profile (such as upload as supplementary material for ## Input samplesheet -### Fastq input samplesheet (bulk sequencing) +### Fastq input samplesheet (bulk AIRR sequencing) The required input file for processing raw BCR or TCR bulk targeted sequencing data is a sample sheet in TSV format (tab separated). The columns `sample_id`, `filename_R1`, `filename_R2`, `subject_id`, `species`, `tissue`, `pcr_target_locus`, `single_cell`, `sex`, `age` and `biomaterial_provider` are required. An example samplesheet is: @@ -143,7 +143,7 @@ The required input file for processing raw BCR or TCR bulk targeted sequencing d - `age`: Subject biological age. - `single_cell`: TRUE or FALSE. -Other optional columns can be added. These columns will be available when building the contrasts for the repertoire comparison report. It is recommended that these columns also follow the AIRR nomenclature. Examples are: +Other optional columns can be added. These columns will be available as metadata in the final repertoire table. It is recommended that these columns also follow the AIRR nomenclature. Examples are: - `intervention`: Description of intervention. - `disease_diagnosis`: Diagnosis of subject. @@ -151,19 +151,19 @@ Other optional columns can be added. These columns will be available when buildi - `collection_time_point_reference`: Event in the study schedule to which `Sample collection time` relates to (e.g. primary vaccination, intervention start). - `cell_subset`: Commonly-used designation of isolated cell population. -The metadata specified in the input file will then be automatically annotated in a column with the same header in the tables generated by the pipeline. +It is possible to provide several fastq files per sample (e.g. sequenced over different chips or lanes). In this case the different fastq files per sample will be merged together prior to processing. Provide one fastq pair R1/R2 per row, and the same `sample_id` field for these rows. ### Fastq input samplesheet (single cell sequencing) -The required input file for processing raw BCR or TCR single cell targeted sequencing data is a sample sheet in TSV format (tab separated). The columns `sample_id`, `filename_R1`, `filename_R2`, `subject_id`, `species`, `tissue`, `pcr_target_locus`, `single_cell`, `sex`, `age` and `biomaterial_provider` are required. You can refer to the bulk fastq input section for documentation on the individual columns. +The required input file for processing raw BCR or TCR single cell targeted sequencing data is a sample sheet in TSV format (tab separated). The columns `sample_id`, `filename_R1`, `filename_R2`, `subject_id`, `species`, `tissue`, `pcr_target_locus`, `single_cell`, `sex`, `age` and `biomaterial_provider` are required. Any other columns you add will be available in the final repertoire file as extra metadata fields. You can refer to the bulk fastq input section for documentation on the individual columns. An example samplesheet is: -| sample_id | filename_R1 | filename_R2 | subject_id | species | pcr_target_locus | tissue | sex | age | biomaterial_provider | single_cell | intervention | collection_time_point_relative | cell_subset | -| --------- | ------------------------------- | ------------------------------- | ---------- | ------- | ---------------- | ------ | ------ | --- | -------------------- | ----------- | -------------- | ------------------------------ | ------------ | -| sample01 | sample1_S1_L001_R1_001.fastq.gz | sample1_S1_L001_R2_001.fastq.gz | Subject02 | human | IG | blood | NA | 53 | sequencing_facility | FALSE | Drug_treatment | Baseline | plasmablasts | -| sample02 | sample2_S1_L001_R1_001.fastq.gz | sample2_S1_L001_R2_001.fastq.gz | Subject02 | human | TR | blood | female | 78 | sequencing_facility | FALSE | Drug_treatment | Baseline | plasmablasts | +| sample_id | filename_R1 | filename_R2 | subject_id | species | pcr_target_locus | tissue | sex | age | biomaterial_provider | single_cell | +| --------- | -------------------------------- | -------------------------------- | ---------- | ------- | ---------------- | ------ | ------ | --- | -------------------- | ----------- | +| sample01 | sample01_S1_L001_R1_001.fastq.gz | sample01_S1_L001_R2_001.fastq.gz | Subject02 | human | IG | blood | NA | 53 | sequencing_facility | TRUE | +| sample02 | sample02_S1_L001_R1_001.fastq.gz | sample02_S1_L001_R2_001.fastq.gz | Subject02 | human | TR | blood | female | 78 | sequencing_facility | TRUE | -> FASTQ files must confirm the 10xGenomics cellranger naming conventions
>**`[SAMPLE-NAME]`_S1_L00`[LANE-NUMBER]` _`[READ-TYPE]`\_001.fastq.gz** +> FASTQ files must conform with the 10xGenomics cellranger naming conventions with the same sample name as provided in the sample*id column
>\*\*`[SAMPLE-NAME]`* S`[CHIP-NUMBER]`_ L00`[LANE-NUMBER]`_`[R1/R2]`\_001.fastq.gz\*\* > > Read type is one of > @@ -172,6 +172,13 @@ An example samplesheet is: > - `R1`: Read 1 > - `R2`: Read 2 +It is possible to provide several fastq files per sample (e.g. sequenced over different chips or lanes). In this case the different fastq files per sample will be provided to the same cellranger process. These rows should then have an identical `sample_id` field. + +### Fastq input samplesheet (untargeted bulk or sc RNA sequencing) + +When running the untargeted protocol, BCR or TCR sequences will be extracted from the untargeted bulk or single-cell RNA sequencing with tools such as [TRUST4](https://github.com/liulab-dfci/TRUST4). +The required input file is the same as for the [Fastq bulk AIRR samplesheet](#fastq-input-samplesheet-bulk-airr-sequencing) or [Fastq single-cell AIRR samplesheet](#fastq-input-samplesheet-single-cell-sequencing) depending on the input data type (bulk RNAseq or single-cell RNAseq). + ### Assembled input samplesheet (bulk or single-cell sequencing) The required input file for processing raw BCR or TCR bulk targeted sequencing data is a sample sheet in TSV format (tab separated). The columns `sample_id`, `filename`, `subject_id`, `species`, `tissue`, `single_cell`, `sex`, `age` and `biomaterial_provider` are required. All fields are explained in the previous section, with the only difference being that there is only one `filename` column for the assembled input samplesheet. The provided file will be different from assembled single-cell or bulk data: @@ -243,7 +250,7 @@ And similarly for TCR libraries: ```bash nextflow run nf-core/airrflow -r \ --profile nebnext_umi_bcr,docker \ +-profile nebnext_umi_tcr,docker \ --input input_samplesheet.tsv \ --cprimers https://bitbucket.org/kleinstein/immcantation/raw/354f49228a43b4c2858d67fb09886126b314e317/protocols/AbSeq/AbSeq_R1_Mouse_TR_Primers.fasta \ --internal_cregion_sequences https://bitbucket.org/kleinstein/immcantation/raw/354f49228a43b4c2858d67fb09886126b314e317/protocols/AbSeq/AbSeq_Mouse_TR_InternalCRegion.fasta \ @@ -468,6 +475,43 @@ nextflow run nf-core/airrflow -r dev \ - The 10xGenomics reference can be downloaded from the [download page](https://www.10xgenomics.com/support/software/cell-ranger/downloads) - To generate a V(D)J segment fasta file as reference from IMGT one can follow the [cellranger docs](https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references#imgt). +## Supported unselected RNA-seq based methods + +nf-core/airrflow supports unselected bulk or single-cell RNA-seq fastq files as input. [TRUST4](https://github.com/liulab-dfci/TRUST4) is used to extract TCR/BCR sequences from these files. The resulting AIRR tables are then fed into airrflow's Immcantation based workflow.
+To use unselected RNA-seq based input, specify `--library_generation_method trust4`. + +### Bulk RNA-seq + +A typical command to run the pipeline from **bulk RNA-seq fastq files** is: + +```bash +nextflow run nf-core/airrfow \ +-profile \ +--mode fastq \ +--input input_samplesheet.tsv \ +--library_generation_method trust4 \ +--outdir results +``` + +### Single-cell RNA-seq + +A typical command to run the pipeline from **single-cell RNA-seq fastq files** is: + +```bash +nextflow run nf-core/airrfow \ +-profile \ +--mode fastq \ +--input input_samplesheet.tsv \ +--library_generation_method trust4 \ +--umi_read R1 \ +--cell_barcode_read R1 \ +--read_format bc:0:15,um:16:27 \ +--outdir results +``` + +- If UMI's are present, the read containing them must be specified using the `--umi_read` parameter. +- The `--read_format` parameter can be used to specify the Cell Barcode and UMI position within the reads (see TRUST4 [docs](https://github.com/liulab-dfci/TRUST4?tab=readme-ov-file#10x-genomics-data-and-barcode-based-single-cell-data)). For scRNAseq with 10X Genomics the R1 read usually contains both the cell barcode (barcode) and UMI. So we specify "R1" for both `--umi_read` and `--cell_barcode_read`, and the positions of both the cell barcode and UMI with the `--read_format` parameter as in the example ("bc:0:15,um:16:27"). Then specify the R1 read in the filename_R1 column of the samplesheet, and the read containing the actual sequence (usually R2) in the filename_R2 column of the samplesheet. + ## Core Nextflow arguments :::note diff --git a/main.nf b/main.nf index 2f2ca54a..2d174a8c 100644 --- a/main.nf +++ b/main.nf @@ -9,8 +9,6 @@ ---------------------------------------------------------------------------------------- */ -nextflow.enable.dsl = 2 - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS @@ -20,7 +18,6 @@ nextflow.enable.dsl = 2 include { AIRRFLOW } from './workflows/airrflow' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_airrflow_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_airrflow_pipeline' - include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_airrflow_pipeline' /* @@ -52,10 +49,8 @@ workflow NFCORE_AIRRFLOW { AIRRFLOW ( samplesheet ) - emit: multiqc_report = AIRRFLOW.out.multiqc_report // channel: /path/to/multiqc_report.html - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -66,13 +61,11 @@ workflow NFCORE_AIRRFLOW { workflow { main: - // // SUBWORKFLOW: Run initialisation tasks // PIPELINE_INITIALISATION ( params.version, - params.help, params.validate_params, params.monochrome_logs, args, @@ -86,7 +79,6 @@ workflow { NFCORE_AIRRFLOW ( PIPELINE_INITIALISATION.out.samplesheet ) - // // SUBWORKFLOW: Run completion tasks // diff --git a/modules.json b/modules.json index 3a6e053c..f04d35d8 100644 --- a/modules.json +++ b/modules.json @@ -17,7 +17,7 @@ }, "cellranger/vdj": { "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "fastp": { @@ -27,12 +27,17 @@ }, "fastqc": { "branch": "master", - "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d", + "installed_by": ["modules"] + }, + "trust4": { + "branch": "master", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } } @@ -41,17 +46,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", + "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba", "installed_by": ["subworkflows"] }, - "utils_nfvalidation_plugin": { + "utils_nfschema_plugin": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", "installed_by": ["subworkflows"] } } diff --git a/modules/local/airrflow_report/airrflow_report.nf b/modules/local/airrflow_report/airrflow_report.nf index 990e492e..5931831b 100644 --- a/modules/local/airrflow_report/airrflow_report.nf +++ b/modules/local/airrflow_report/airrflow_report.nf @@ -5,7 +5,7 @@ process AIRRFLOW_REPORT { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" input: tuple val(meta), path(tab) // sequence tsv table in AIRR format diff --git a/modules/local/changeo/changeo_makedb.nf b/modules/local/changeo/changeo_makedb.nf index 4862ba86..d0dadc66 100644 --- a/modules/local/changeo/changeo_makedb.nf +++ b/modules/local/changeo/changeo_makedb.nf @@ -21,10 +21,11 @@ process CHANGEO_MAKEDB { script: def args = task.ext.args ?: '' + def partial = meta.species.toLowerCase()=='mouse' && meta.locus.toLowerCase()=='tr' ? '--partial' : '' """ MakeDb.py igblast -i $igblast -s $reads -r \\ ${reference_fasta}/${meta.species.toLowerCase()}/vdj/ \\ - $args \\ + $args $partial \\ --outname ${meta.id} > ${meta.id}_makedb_command_log.txt cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/changeo/changeo_parsedb_select.nf b/modules/local/changeo/changeo_parsedb_select_locus.nf similarity index 72% rename from modules/local/changeo/changeo_parsedb_select.nf rename to modules/local/changeo/changeo_parsedb_select_locus.nf index 2bba4916..32805c26 100644 --- a/modules/local/changeo/changeo_parsedb_select.nf +++ b/modules/local/changeo/changeo_parsedb_select_locus.nf @@ -1,4 +1,4 @@ -process CHANGEO_PARSEDB_SELECT { +process CHANGEO_PARSEDB_SELECT_LOCUS { tag "$meta.id" label 'process_low' label 'immcantation' @@ -18,25 +18,21 @@ process CHANGEO_PARSEDB_SELECT { path "versions.yml" , emit: versions script: - def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' if (meta.locus.toUpperCase() == 'IG'){ """ - ParseDb.py select -d $tab $args --outname ${meta.id} > ${meta.id}_select_command_log.txt + ParseDb.py select -d $tab -f locus -u "IG[HKL]" --regex --outname ${meta.id} > ${meta.id}_select_command_log.txt cat <<-END_VERSIONS > versions.yml "${task.process}": - igblastn: \$( igblastn -version | grep -o "igblast[0-9\\. ]\\+" | grep -o "[0-9\\. ]\\+" ) changeo: \$( ParseDb.py --version | awk -F' ' '{print \$2}' ) END_VERSIONS """ } else if (meta.locus.toUpperCase() == 'TR'){ """ - ParseDb.py select -d $tab $args2 --outname ${meta.id} > "${meta.id}_command_log.txt" + ParseDb.py select -d $tab -f locus -u "TR[ABDG]" --regex --outname ${meta.id} > "${meta.id}_command_log.txt" cat <<-END_VERSIONS > versions.yml "${task.process}": - igblastn: \$( igblastn -version | grep -o "igblast[0-9\\. ]\\+" | grep -o "[0-9\\. ]\\+" ) changeo: \$( ParseDb.py --version | awk -F' ' '{print \$2}' ) END_VERSIONS """ diff --git a/modules/local/changeo/changeo_parsedb_split.nf b/modules/local/changeo/changeo_parsedb_split.nf index f67405bb..af950a77 100644 --- a/modules/local/changeo/changeo_parsedb_split.nf +++ b/modules/local/changeo/changeo_parsedb_split.nf @@ -13,7 +13,8 @@ process CHANGEO_PARSEDB_SPLIT { tuple val(meta), path(tab) // sequence tsv in AIRR format output: - tuple val(meta), path("*productive-T.tsv"), emit: tab // sequence tsv in AIRR format + tuple val(meta), path("*productive-T.tsv"), emit: tab //sequence tsv in AIRR format + tuple val(meta), path("*productive-F.tsv"), emit: unproductive, optional: true //optional non-productive sequences path("*_command_log.txt"), emit: logs //process logs path "versions.yml" , emit: versions diff --git a/modules/local/enchantr/collapse_duplicates.nf b/modules/local/enchantr/collapse_duplicates.nf index 618491ab..afd346dc 100644 --- a/modules/local/enchantr/collapse_duplicates.nf +++ b/modules/local/enchantr/collapse_duplicates.nf @@ -7,7 +7,7 @@ process COLLAPSE_DUPLICATES { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" input: tuple val(meta), path(tabs) // tuple [val(meta), sequence tsv in AIRR format ] diff --git a/modules/local/enchantr/define_clones.nf b/modules/local/enchantr/define_clones.nf index ae71b900..f234da66 100644 --- a/modules/local/enchantr/define_clones.nf +++ b/modules/local/enchantr/define_clones.nf @@ -24,7 +24,7 @@ process DEFINE_CLONES { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" input: tuple val(meta), path(tabs) // meta, sequence tsv in AIRR format @@ -59,7 +59,6 @@ process DEFINE_CLONES { 'threshold'=${thr}, \\ 'singlecell'='${params.singlecell}', \\ 'outdir'=getwd(), \\ - 'isotype_column'='${params.isotype_column}', \\ 'nproc'=${task.cpus}, \\ 'log'='${meta.id}_clone_command_log' ${args}))" diff --git a/modules/local/enchantr/detect_contamination.nf b/modules/local/enchantr/detect_contamination.nf index cec4deca..3716a8c3 100644 --- a/modules/local/enchantr/detect_contamination.nf +++ b/modules/local/enchantr/detect_contamination.nf @@ -8,7 +8,7 @@ process DETECT_CONTAMINATION { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" input: path(tabs) diff --git a/modules/local/enchantr/dowser_lineages.nf b/modules/local/enchantr/dowser_lineages.nf index 0559c496..2c92d290 100644 --- a/modules/local/enchantr/dowser_lineages.nf +++ b/modules/local/enchantr/dowser_lineages.nf @@ -24,7 +24,7 @@ process DOWSER_LINEAGES { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" input: tuple val(meta), path(tabs) diff --git a/modules/local/enchantr/find_threshold.nf b/modules/local/enchantr/find_threshold.nf index 4a9b0ab0..ecaf072f 100644 --- a/modules/local/enchantr/find_threshold.nf +++ b/modules/local/enchantr/find_threshold.nf @@ -24,7 +24,7 @@ process FIND_THRESHOLD { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" input: diff --git a/modules/local/enchantr/remove_chimeric.nf b/modules/local/enchantr/remove_chimeric.nf index 2df7e60c..b2b53073 100644 --- a/modules/local/enchantr/remove_chimeric.nf +++ b/modules/local/enchantr/remove_chimeric.nf @@ -8,7 +8,7 @@ process REMOVE_CHIMERIC { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" input: diff --git a/modules/local/enchantr/report_file_size.nf b/modules/local/enchantr/report_file_size.nf index 093a9e61..a198f47f 100644 --- a/modules/local/enchantr/report_file_size.nf +++ b/modules/local/enchantr/report_file_size.nf @@ -9,7 +9,7 @@ process REPORT_FILE_SIZE { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" input: path logs diff --git a/modules/local/enchantr/single_cell_qc.nf b/modules/local/enchantr/single_cell_qc.nf index 4170e51b..c331f70a 100644 --- a/modules/local/enchantr/single_cell_qc.nf +++ b/modules/local/enchantr/single_cell_qc.nf @@ -23,7 +23,7 @@ process SINGLE_CELL_QC { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" input: path(tabs) diff --git a/modules/local/enchantr/validate_input.nf b/modules/local/enchantr/validate_input.nf index 6ec12543..754a5c54 100644 --- a/modules/local/enchantr/validate_input.nf +++ b/modules/local/enchantr/validate_input.nf @@ -9,7 +9,7 @@ process VALIDATE_INPUT { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" input: file samplesheet diff --git a/modules/local/parse_logs.nf b/modules/local/parse_logs.nf index f811e427..8f4fb052 100644 --- a/modules/local/parse_logs.nf +++ b/modules/local/parse_logs.nf @@ -18,7 +18,7 @@ process PARSE_LOGS { path('assemble_pairs/*') //PRESTO_ASSEMBLEPAIRS logs path('deduplicates/*') //PRESTO_COLLAPSESEQ logs path('filter_representative_2/*') //PRESTO_SPLITSEQ logs - path('igblast/*') //CHANGEO_PARSEDB_SELECT logs + path('igblast/*') //CHANGEO_MAKEDB logs path('metadata.tsv') //METADATA output: diff --git a/modules/local/prepare_trust4_reference.nf b/modules/local/prepare_trust4_reference.nf new file mode 100644 index 00000000..e0c2306c --- /dev/null +++ b/modules/local/prepare_trust4_reference.nf @@ -0,0 +1,24 @@ +process PREPARE_TRUST4_REFERENCE { + tag "$meta.id" + label 'process_medium' + + conda "bioconda::trust4=1.0.13" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/trust4:1.0.13--h43eeafb_0': + 'biocontainers/trust4:1.0.13--h43eeafb_0' }" + + input: + tuple val(meta), path(R1), path(R2) + path(reference_igblast) + + output: + path("trust4_reference.fa") , emit: trust4_reference + + script: + """ + cat ${reference_igblast}/fasta/imgt_${meta.species.toLowerCase()}_*.fasta \\ + ${reference_igblast}/fasta/imgt_${meta.species.toLowerCase()}_*.fasta >> trust4_reference.fa + """ + + +} diff --git a/modules/local/presto/presto_assemblepairs.nf b/modules/local/presto/presto_assemblepairs.nf index c6ba4287..e108f62a 100644 --- a/modules/local/presto/presto_assemblepairs.nf +++ b/modules/local/presto/presto_assemblepairs.nf @@ -14,7 +14,6 @@ process PRESTO_ASSEMBLEPAIRS { output: tuple val(meta), path("*_assemble-pass.fastq"), emit: reads path("*_command_log.txt"), emit: logs - path("*.log") path("*_table.tab") path "versions.yml" , emit: versions diff --git a/modules/local/presto/presto_assemblepairs_sequential.nf b/modules/local/presto/presto_assemblepairs_sequential.nf index 7d9cabb0..b47b9098 100644 --- a/modules/local/presto/presto_assemblepairs_sequential.nf +++ b/modules/local/presto/presto_assemblepairs_sequential.nf @@ -15,7 +15,6 @@ process PRESTO_ASSEMBLEPAIRS_SEQUENTIAL { output: tuple val(meta), path("*_assemble-pass.fastq"), emit: reads path("*_command_log.txt"), emit: logs - path("*.log") path("*_table.tab") path "versions.yml" , emit: versions diff --git a/modules/local/presto/presto_buildconsensus.nf b/modules/local/presto/presto_buildconsensus.nf index 2a85c3ea..9e6c6c4d 100644 --- a/modules/local/presto/presto_buildconsensus.nf +++ b/modules/local/presto/presto_buildconsensus.nf @@ -14,19 +14,16 @@ process PRESTO_BUILDCONSENSUS { output: tuple val(meta), path("*_R1_consensus-pass.fastq"), path("*_R2_consensus-pass.fastq"), emit: reads path("*_command_log.txt"), emit: logs - path("*_R1.log") - path("*_R2.log") path("*.tab"), emit: log_tab path "versions.yml" , emit: versions script: - def barcode_field = params.cluster_sets ? 'CLUSTER' : 'BARCODE' def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def args3 = task.ext.args3 ?: '' """ - BuildConsensus.py -s $R1 --bf ${barcode_field} --nproc ${task.cpus} --prcons ${params.primer_consensus} --maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap} ${args} --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log.txt - BuildConsensus.py -s $R2 --bf ${barcode_field} --nproc ${task.cpus} --prcons ${params.primer_consensus} --maxerror ${params.buildconsensus_maxerror} --maxgap ${params.buildconsensus_maxgap} ${args2} --outname ${meta.id}_R2 --log ${meta.id}_R2.log >> ${meta.id}_command_log.txt + BuildConsensus.py -s $R1 --nproc ${task.cpus} ${args} --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log.txt + BuildConsensus.py -s $R2 --nproc ${task.cpus} ${args2} --outname ${meta.id}_R2 --log ${meta.id}_R2.log >> ${meta.id}_command_log.txt ParseLog.py -l ${meta.id}_R1.log ${meta.id}_R2.log ${args3} cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/presto/presto_clustersets.nf b/modules/local/presto/presto_clustersets.nf index 32061f0e..71868b5b 100644 --- a/modules/local/presto/presto_clustersets.nf +++ b/modules/local/presto/presto_clustersets.nf @@ -14,15 +14,16 @@ process PRESTO_CLUSTERSETS { output: tuple val(meta), path("*_R1_cluster-pass.fastq"), path("*_R2_cluster-pass.fastq"), emit: reads path "*_command_log.txt", emit: logs - path "*.log" path "*.tab", emit: log_tab path("versions.yml"), emit: versions script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' """ - ClusterSets.py set --nproc ${task.cpus} -s $R1 --outname ${meta.id}_R1 --exec vsearch --log ${meta.id}_R1.log > ${meta.id}_command_log.txt - ClusterSets.py set --nproc ${task.cpus} -s $R2 --outname ${meta.id}_R2 --exec vsearch --log ${meta.id}_R2.log >> ${meta.id}_command_log.txt - ParseLog.py -l ${meta.id}_R1.log ${meta.id}_R2.log -f ID BARCODE SEQCOUNT CLUSTERS + ClusterSets.py set --nproc ${task.cpus} -s $R1 --outname ${meta.id}_R1 $args --log ${meta.id}_R1.log > ${meta.id}_command_log.txt + ClusterSets.py set --nproc ${task.cpus} -s $R2 --outname ${meta.id}_R2 $args --log ${meta.id}_R2.log >> ${meta.id}_command_log.txt + ParseLog.py -l ${meta.id}_R1.log ${meta.id}_R2.log $args2 cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/presto/presto_collapseseq.nf b/modules/local/presto/presto_collapseseq.nf index efbe4def..84177805 100644 --- a/modules/local/presto/presto_collapseseq.nf +++ b/modules/local/presto/presto_collapseseq.nf @@ -14,7 +14,6 @@ process PRESTO_COLLAPSESEQ { output: tuple val(meta), path("*_collapse-unique.fastq") , emit: reads path("*_command_log.txt") , emit: logs - path("*.log") path("*_table.tab") path("versions.yml"), emit: versions diff --git a/modules/local/presto/presto_filterseq.nf b/modules/local/presto/presto_filterseq.nf index a7733147..ee474865 100644 --- a/modules/local/presto/presto_filterseq.nf +++ b/modules/local/presto/presto_filterseq.nf @@ -15,8 +15,6 @@ process PRESTO_FILTERSEQ { tuple val(meta), path("*R1_quality-pass.fastq"), path("*R2_quality-pass.fastq") , emit: reads path "*_command_log_R?.txt" , emit: logs path "versions.yml" , emit: versions - path "*_R1.log" - path "*_R2.log" path "*.tab" , emit: log_tab script: diff --git a/modules/local/presto/presto_filterseq_postassembly.nf b/modules/local/presto/presto_filterseq_postassembly.nf index 0f821f5b..45dfea17 100644 --- a/modules/local/presto/presto_filterseq_postassembly.nf +++ b/modules/local/presto/presto_filterseq_postassembly.nf @@ -15,7 +15,6 @@ process PRESTO_FILTERSEQ_POSTASSEMBLY { tuple val(meta), path("*quality-pass.fastq") , emit: reads path "*_command_log.txt" , emit: logs path "versions.yml" , emit: versions - path "*.log" path "*.tab" , emit: log_tab script: diff --git a/modules/local/presto/presto_maskprimers.nf b/modules/local/presto/presto_maskprimers.nf index 48e66a84..26c88854 100644 --- a/modules/local/presto/presto_maskprimers.nf +++ b/modules/local/presto/presto_maskprimers.nf @@ -16,8 +16,6 @@ process PRESTO_MASKPRIMERS { output: tuple val(meta), path("*_R1_primers-pass.fastq"), path("*_R2_primers-pass.fastq") , emit: reads path "*_command_log_R?.txt", emit: logs - path "*_R1.log" - path "*_R2.log" path "*.tab", emit: log_tab path "versions.yml" , emit: versions @@ -28,8 +26,8 @@ process PRESTO_MASKPRIMERS { def primer_start_R1 = (params.index_file | params.umi_position == 'R1') ? "--start ${params.umi_length + params.cprimer_start} --barcode" : "--start ${params.cprimer_start}" def primer_start_R2 = (params.umi_position == 'R2') ? "--start ${params.umi_length + params.vprimer_start} --barcode" : "--start ${params.vprimer_start}" """ - MaskPrimers.py score --nproc ${task.cpus} -s $R1 -p ${cprimers} $primer_start_R1 $revpr --maxerror ${params.primer_r1_maxerror} --mode ${params.primer_mask_mode} --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log_R1.txt - MaskPrimers.py score --nproc ${task.cpus} -s $R2 -p ${vprimers} $primer_start_R2 $revpr --maxerror ${params.primer_r2_maxerror} --mode ${params.primer_mask_mode} --outname ${meta.id}_R2 --log ${meta.id}_R2.log > ${meta.id}_command_log_R2.txt + MaskPrimers.py score --nproc ${task.cpus} -s $R1 -p ${cprimers} $primer_start_R1 $revpr --maxerror ${params.primer_r1_maxerror} --mode ${params.primer_r1_mask_mode} --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log_R1.txt + MaskPrimers.py score --nproc ${task.cpus} -s $R2 -p ${vprimers} $primer_start_R2 $revpr --maxerror ${params.primer_r2_maxerror} --mode ${params.primer_r2_mask_mode} --outname ${meta.id}_R2 --log ${meta.id}_R2.log > ${meta.id}_command_log_R2.txt ParseLog.py -l ${meta.id}_R1.log ${meta.id}_R2.log -f ID PRIMER ERROR cat <<-END_VERSIONS > versions.yml @@ -41,8 +39,8 @@ process PRESTO_MASKPRIMERS { def primer_start_R1 = (params.index_file | params.umi_position == 'R1') ? "--start ${params.umi_length + params.vprimer_start} --barcode" : "--start ${params.vprimer_start}" def primer_start_R2 = (params.umi_position == 'R2') ? "--start ${params.umi_length + params.cprimer_start} --barcode" : "--start ${params.cprimer_start}" """ - MaskPrimers.py score --nproc ${task.cpus} -s $R1 -p ${vprimers} $primer_start_R1 $revpr --maxerror ${params.primer_r1_maxerror} --mode ${params.primer_mask_mode} --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log_R1.txt - MaskPrimers.py score --nproc ${task.cpus} -s $R2 -p ${cprimers} $primer_start_R2 $revpr --maxerror ${params.primer_r2_maxerror} --mode ${params.primer_mask_mode} --outname ${meta.id}_R2 --log ${meta.id}_R2.log > ${meta.id}_command_log_R2.txt + MaskPrimers.py score --nproc ${task.cpus} -s $R1 -p ${vprimers} $primer_start_R1 $revpr --maxerror ${params.primer_r1_maxerror} --mode ${params.primer_r1_mask_mode} --outname ${meta.id}_R1 --log ${meta.id}_R1.log > ${meta.id}_command_log_R1.txt + MaskPrimers.py score --nproc ${task.cpus} -s $R2 -p ${cprimers} $primer_start_R2 $revpr --maxerror ${params.primer_r2_maxerror} --mode ${params.primer_r2_mask_mode} --outname ${meta.id}_R2 --log ${meta.id}_R2.log > ${meta.id}_command_log_R2.txt ParseLog.py -l "${meta.id}_R1.log" "${meta.id}_R2.log" -f ID PRIMER ERROR cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/presto/presto_maskprimers_align.nf b/modules/local/presto/presto_maskprimers_align.nf index 055e5d93..dce835dc 100644 --- a/modules/local/presto/presto_maskprimers_align.nf +++ b/modules/local/presto/presto_maskprimers_align.nf @@ -10,32 +10,37 @@ process PRESTO_MASKPRIMERS_ALIGN { input: tuple val(meta), path(R1) - path(cprimers) + path(primers) val(max_len) + val(barcode) val(max_error) val(mask_mode) + val(reverse_primers) + val(suffix) output: - tuple val(meta), path("*_R1_primers-pass.fastq") , emit: reads - path "*_command_log_R1.txt", emit: logs - path "*_R1.log" + tuple val(meta), path("*_primers-pass.fastq") , emit: reads + path "*.txt", emit: logs path "*.tab", emit: log_tab path "versions.yml" , emit: versions script: + def barcode = barcode ? '--barcode' : '' + def revpr = reverse_primers ? '--revpr' : '' def args = task.ext.args?: '' def args2 = task.ext.args2?: '' """ MaskPrimers.py align --nproc ${task.cpus} \\ -s $R1 \\ - -p ${cprimers} \\ + -p ${primers} \\ --maxlen ${max_len} \\ --maxerror ${max_error} \\ --mode ${mask_mode} \\ + $barcode \\ $args \\ - --outname ${meta.id}_R1 \\ - --log ${meta.id}_R1.log > ${meta.id}_command_log_R1.txt - ParseLog.py -l ${meta.id}_R1.log $args2 + --outname ${meta.id}_${suffix} \\ + --log ${meta.id}_${suffix}.log > ${meta.id}_command_log_${suffix}.txt + ParseLog.py -l ${meta.id}_${suffix}.log $args2 cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/presto/presto_maskprimers_extract.nf b/modules/local/presto/presto_maskprimers_extract.nf index 661389e0..fad8d624 100644 --- a/modules/local/presto/presto_maskprimers_extract.nf +++ b/modules/local/presto/presto_maskprimers_extract.nf @@ -9,28 +9,35 @@ process PRESTO_MASKPRIMERS_EXTRACT { 'biocontainers/presto:0.7.1--pyhdfd78af_0' }" input: - tuple val(meta), path(R2) + tuple val(meta), path(read) + val(extract_start) + val(extract_length) + val(extract_mode) + val(barcode) + val(suffix) output: - tuple val(meta), path("*_R2_primers-pass.fastq") , emit: reads - path "*_command_log_R2.txt", emit: logs - path "*_R2.log" + tuple val(meta), path("*_primers-pass.fastq") , emit: reads + path "*.txt", emit: logs path "*.tab", emit: log_tab path "versions.yml" , emit: versions script: def args = task.ext.args?: '' def args2 = task.ext.args2?: '' + def barcode = barcode ? '--barcode' : '' """ - MaskPrimers.py extract --nproc ${task.cpus} \\ - -s $R2 \\ - --start ${params.umi_length} \\ - --len ${params.primer_extract_len} \\ + MaskPrimers.py extract \\ + --nproc ${task.cpus} \\ + -s $read \\ + --start ${extract_start} \\ + --len ${extract_length} \\ + $barcode \\ $args \\ - --mode ${params.primer_mask_mode} \\ - --outname ${meta.id}_R2 \\ - --log ${meta.id}_R2.log >> ${meta.id}_command_log_R2.txt - ParseLog.py -l ${meta.id}_R2.log $args2 + --mode ${extract_mode} \\ + --outname ${meta.id}_${suffix} \\ + --log ${meta.id}_${suffix}.log >> ${meta.id}_command_log_${suffix}.txt + ParseLog.py -l *.log $args2 cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/local/presto/presto_maskprimers_postassembly.nf b/modules/local/presto/presto_maskprimers_postassembly.nf index 91427c90..ef5cd4c7 100644 --- a/modules/local/presto/presto_maskprimers_postassembly.nf +++ b/modules/local/presto/presto_maskprimers_postassembly.nf @@ -16,7 +16,6 @@ process PRESTO_MASKPRIMERS_POSTASSEMBLY { output: tuple val(meta), path("*REV_primers-pass.fastq") , emit: reads path "*command_log.txt", emit: logs - path "*.log" path "*.tab", emit: log_tab path "versions.yml" , emit: versions @@ -25,10 +24,10 @@ process PRESTO_MASKPRIMERS_POSTASSEMBLY { if (params.cprimer_position == "R1") { """ MaskPrimers.py score --nproc ${task.cpus} -s $reads -p ${cprimers} --start ${params.cprimer_start} --maxerror ${params.primer_r1_maxerror} \ - --mode ${params.primer_mask_mode} --outname ${meta.id}-FWD \ + --mode ${params.primer_r1_mask_mode} --outname ${meta.id}-FWD \ --log ${meta.id}-FWD.log > ${meta.id}_command_log.txt MaskPrimers.py score --nproc ${task.cpus} -s ${meta.id}-FWD_primers-pass.fastq -p ${vprimers} --start ${params.vprimer_start} --maxerror ${params.primer_r2_maxerror} \ - --mode ${params.primer_mask_mode} --outname ${meta.id}-REV $revpr \ + --mode ${params.primer_r2_mask_mode} --outname ${meta.id}-REV $revpr \ --log ${meta.id}-REV.log >> ${meta.id}_command_log.txt ParseLog.py -l ${meta.id}-FWD.log ${meta.id}-REV.log -f ID PRIMER ERROR @@ -40,10 +39,10 @@ process PRESTO_MASKPRIMERS_POSTASSEMBLY { } else if (params.cprimer_position == "R2") { """ MaskPrimers.py score --nproc ${task.cpus} -s $reads -p ${vprimers} --start ${params.vprimer_start} --maxerror ${params.primer_r1_maxerror} \ - --mode ${params.primer_mask_mode} --outname ${meta.id}-FWD \ + --mode ${params.primer_r1_mask_mode} --outname ${meta.id}-FWD \ --log ${meta.id}-FWD.log > ${meta.id}_command_log.txt MaskPrimers.py score --nproc ${task.cpus} -s ${meta.id}-FWD_primers-pass.fastq -p ${cprimers} --start ${params.cprimer_start} --maxerror ${params.primer_r2_maxerror} \ - --mode ${params.primer_mask_mode} --outname ${meta.id}-REV $revpr \ + --mode ${params.primer_r2_mask_mode} --outname ${meta.id}-REV $revpr \ --log ${meta.id}-REV.log >> ${meta.id}_command_log.txt ParseLog.py -l ${meta.id}-FWD.log ${meta.id}-REV.log -f ID PRIMER ERROR diff --git a/modules/local/presto/presto_maskprimers_score.nf b/modules/local/presto/presto_maskprimers_score.nf new file mode 100644 index 00000000..77b90cfc --- /dev/null +++ b/modules/local/presto/presto_maskprimers_score.nf @@ -0,0 +1,52 @@ +process PRESTO_MASKPRIMERS_SCORE { + tag "$meta.id" + label "process_high" + label 'immcantation' + + conda "bioconda::presto=0.7.1" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/presto:0.7.1--pyhdfd78af_0' : + 'biocontainers/presto:0.7.1--pyhdfd78af_0' }" + + input: + tuple val(meta), path(read) + path(primers) + val(primer_start) + val(barcode) + val(primer_maxerror) + val(primer_mask_mode) + val(reverse_primers) + val(suffix) + + output: + tuple val(meta), path("*_primers-pass.fastq"), emit: reads + path "*.txt", emit: logs + path "*.tab", emit: log_tab + path "versions.yml" , emit: versions + + + script: + def args = task.ext.args?: '' + def args2 = task.ext.args2?: '' + def revpr = reverse_primers ? '--revpr' : '' + def barcode = barcode ? '--barcode' : '' + """ + MaskPrimers.py score \\ + --nproc ${task.cpus} \\ + -s $read \\ + -p ${primers} \\ + --maxerror ${primer_maxerror} \\ + --mode ${primer_mask_mode} \\ + --start ${primer_start} \\ + $barcode $revpr \\ + $args \\ + --outname ${meta.id}_${suffix} \\ + --log ${meta.id}_${suffix}.log > ${meta.id}_command_log_${suffix}.txt + ParseLog.py -l *.log $args2 + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + presto: \$( MaskPrimers.py --version | awk -F' ' '{print \$2}' ) + END_VERSIONS + """ +} diff --git a/modules/local/presto/presto_pairseq.nf b/modules/local/presto/presto_pairseq.nf index 40ac33b1..cbd37cd3 100644 --- a/modules/local/presto/presto_pairseq.nf +++ b/modules/local/presto/presto_pairseq.nf @@ -10,6 +10,7 @@ process PRESTO_PAIRSEQ { input: tuple val(meta), path("${meta.id}_R1.fastq"), path("${meta.id}_R2.fastq") + val(barcode_position) output: tuple val(meta), path("*R1_pair-pass.fastq"), path("*R2_pair-pass.fastq") , emit: reads @@ -17,7 +18,7 @@ process PRESTO_PAIRSEQ { path "versions.yml" , emit: versions script: - def copyfield = (params.index_file | params.umi_position == 'R1') ? "--1f BARCODE" : "--2f BARCODE" + def copyfield = (barcode_position == 'R1')? '--1f BARCODE' : (barcode_position == 'R2')? '--2f BARCODE' : (barcode_position == 'R1R2')? '--1f BARCODE --2f BARCODE' : (barcode_position == 'clustersets')? '--1f CLUSTER --2f CLUSTER' : '' def args = task.ext.args?: '' """ PairSeq.py -1 ${meta.id}_R1.fastq -2 ${meta.id}_R2.fastq $copyfield $args > ${meta.id}_command_log.txt diff --git a/modules/local/reveal/add_meta_to_tab.nf b/modules/local/reveal/add_meta_to_tab.nf index 1c50d60e..889d929e 100644 --- a/modules/local/reveal/add_meta_to_tab.nf +++ b/modules/local/reveal/add_meta_to_tab.nf @@ -6,7 +6,7 @@ process ADD_META_TO_TAB { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" cache 'deep' // Without 'deep' this process would run when using -resume diff --git a/modules/local/reveal/filter_junction_mod3.nf b/modules/local/reveal/filter_junction_mod3.nf index 92ef4833..9408bd2d 100644 --- a/modules/local/reveal/filter_junction_mod3.nf +++ b/modules/local/reveal/filter_junction_mod3.nf @@ -6,7 +6,7 @@ process FILTER_JUNCTION_MOD3 { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" input: tuple val(meta), path(tab) // sequence tsv in AIRR format diff --git a/modules/local/reveal/filter_quality.nf b/modules/local/reveal/filter_quality.nf index 4675ed17..12a79ec6 100644 --- a/modules/local/reveal/filter_quality.nf +++ b/modules/local/reveal/filter_quality.nf @@ -6,7 +6,7 @@ process FILTER_QUALITY { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "nf-core/airrflow currently does not support Conda. Please use a container profile instead." } - container "docker.io/immcantation/airrflow:4.1.0" + container "docker.io/immcantation/airrflow:4.2.0" input: tuple val(meta), path(tab) // sequence tsv in AIRR format diff --git a/modules/nf-core/cellranger/vdj/environment.yml b/modules/nf-core/cellranger/vdj/environment.yml deleted file mode 100644 index 2ddcc0c6..00000000 --- a/modules/nf-core/cellranger/vdj/environment.yml +++ /dev/null @@ -1,5 +0,0 @@ -name: cellranger_vdj -channels: - - conda-forge - - bioconda - - defaults diff --git a/modules/nf-core/cellranger/vdj/main.nf b/modules/nf-core/cellranger/vdj/main.nf index 45a920f0..590d368f 100644 --- a/modules/nf-core/cellranger/vdj/main.nf +++ b/modules/nf-core/cellranger/vdj/main.nf @@ -2,7 +2,7 @@ process CELLRANGER_VDJ { tag "${meta.id}" label 'process_high' - container "nf-core/cellranger:7.1.0" + container "nf-core/cellranger:8.0.0" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/cellranger/vdj/meta.yml b/modules/nf-core/cellranger/vdj/meta.yml index 3f4d7788..8fbd75e8 100644 --- a/modules/nf-core/cellranger/vdj/meta.yml +++ b/modules/nf-core/cellranger/vdj/meta.yml @@ -1,5 +1,6 @@ name: cellranger_vdj -description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling. +description: Module to use Cell Ranger's pipelines analyze sequencing data produced + from Chromium Single Cell Immune Profiling. keywords: - align - vdj @@ -9,40 +10,54 @@ keywords: - cellranger tools: - cellranger: - description: Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe V(D)J Browser. + description: Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger + vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries + and performs sequence assembly and paired clonotype calling. It uses the Chromium + cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes + and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe + V(D)J Browser. homepage: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj tool_dev_url: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj - licence: 10x Genomics EULA + licence: [10X Genomics EULA] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" - - reference: - type: directory - description: Folder containing all the reference indices needed by Cell Ranger + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" + - - reference: + type: directory + description: Folder containing all the reference indices needed by Cell Ranger output: - outs: - type: file - description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list - pattern: "${meta.id}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger, see official 10X Genomics + documentation for a complete list + pattern: "${meta.id}/outs/*" + - "**/outs/**": + type: file + description: Files containing the outputs of Cell Ranger, see official 10X Genomics + documentation for a complete list + pattern: "${meta.id}/outs/*" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - - "@Emiller88" + - "@edmundmiller" - "@klkeys" maintainers: - "@ggabernet" - - "@Emiller88" + - "@edmundmiller" - "@klkeys" diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a..691d4c76 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf index d79f1c86..d8989f48 100644 --- a/modules/nf-core/fastqc/main.nf +++ b/modules/nf-core/fastqc/main.nf @@ -26,7 +26,10 @@ process FASTQC { def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // 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 + // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e0..4827da7a 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,35 +16,44 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 70edae4d..e9d79a07 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,17 +23,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:

Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -54,16 +51,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -83,13 +78,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -109,13 +102,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -138,22 +129,20 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -173,21 +162,18 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } test("sarscov2 single-end [fastq] - stub") { - options "-stub" - + options "-stub" when { process { """ @@ -201,12 +187,123 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } + { assert process.success }, + { assert snapshot(process.out).match() } ) } } + test("sarscov2 paired-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 interleaved [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [bam] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 multiple [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 custom_prefix - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 86f7c311..d5db3092 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,88 +1,392 @@ { - "fastqc_versions_interleaved": { + "sarscov2 custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:07.293713" + "timestamp": "2024-07-22T11:02:16.374038" }, - "fastqc_stub": { + "sarscov2 single-end [fastq] - stub": { "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:24.993809" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:31:01.425198" + "timestamp": "2024-07-22T11:03:10.93942" }, - "fastqc_versions_multiple": { + "sarscov2 interleaved [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:55.797907" + "timestamp": "2024-07-22T11:01:42.355718" }, - "fastqc_versions_bam": { + "sarscov2 paired-end [bam]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:26.795862" + "timestamp": "2024-07-22T11:01:53.276274" }, - "fastqc_versions_single": { + "sarscov2 multiple [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:27.043675" + "timestamp": "2024-07-22T11:02:05.527626" }, - "fastqc_versions_paired": { + "sarscov2 paired-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:31.188871" + }, + "sarscov2 paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:34.273566" + }, + "sarscov2 multiple [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:47.584191" + "timestamp": "2024-07-22T11:03:02.304411" }, - "fastqc_versions_custom_prefix": { + "sarscov2 single-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:19.095607" + }, + "sarscov2 interleaved [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:44.640184" + }, + "sarscov2 paired-end [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:41:14.576531" + "timestamp": "2024-07-22T11:02:53.550742" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb67..6f5b867b 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352f..cc0643e1 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,16 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml @@ -44,7 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - touch multiqc_plots + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc35..b16c1879 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,40 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242e..33316a7d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { @@ -17,6 +19,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +45,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +72,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd802..2fcbb5ff 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-10-02T17:51:46.317523" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-10-02T17:52:20.680978" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-10-02T17:52:09.185842" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config new file mode 100644 index 00000000..c537a6a3 --- /dev/null +++ b/modules/nf-core/multiqc/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MULTIQC' { + ext.prefix = null + } +} diff --git a/modules/nf-core/trust4/environment.yml b/modules/nf-core/trust4/environment.yml new file mode 100644 index 00000000..7e07e377 --- /dev/null +++ b/modules/nf-core/trust4/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::trust4=1.0.13" diff --git a/modules/nf-core/trust4/main.nf b/modules/nf-core/trust4/main.nf new file mode 100644 index 00000000..1d822fb8 --- /dev/null +++ b/modules/nf-core/trust4/main.nf @@ -0,0 +1,105 @@ +process TRUST4 { + tag "$meta.id" + label 'process_medium' + + conda "bioconda::trust4=1.0.13" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/trust4:1.0.13--h43eeafb_0': + 'biocontainers/trust4:1.0.13--h43eeafb_0' }" + + input: + tuple val(meta), path(bam), path(reads) + tuple val(meta2), path(fasta) + tuple val(meta3), path(vdj_reference) + tuple val(meta4), val(barcode_read) + tuple val(meta5), val(umi_read) + + output: + tuple val(meta), path("*.tsv") , emit: tsv + tuple val(meta), path("*_airr.tsv") , emit: airr_files + tuple val(meta), path("${meta.id}_airr.tsv") , emit: airr_tsv + tuple val(meta), path("*_report.tsv") , emit: report_tsv + tuple val(meta), path("*.fa") , emit: fasta + tuple val(meta), path("*.out") , emit: out + tuple val(meta), path("*.fq") , emit: fq + tuple val(meta), path("**") , emit: outs + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def bam_mode = bam ? "-b ${bam}" : '' + def single_end_mode = reads && meta.single_end ? "-u ${reads}" : '' + // reference is optional for fastq input + def reference = vdj_reference ? "--ref ${vdj_reference}" : "" + // separate forward from reverse pairs + def (forward, reverse) = reads.collate(2).transpose() + def paired_end_mode = reads && (meta.single_end == false) ? "-1 ${forward[0]} -2 ${reverse[0]}" : '' + // read format is optional + def readFormat = params.read_format ? "--readFormat ${params.read_format}" : '' + // add barcode information if present + if (barcode_read) { + if (barcode_read == "R1") { + barcode = "--barcode ${forward[0]}" + } else if (barcode_read == "R2") { + barcode = "--barcode ${reverse[0]}" + } + } + else { + barcode = '' + } + // add umi information if present + if (umi_read) { + if (umi_read == "R1") { + umi = "--UMI ${forward[0]}" + } else if (umi_read == "R2") { + umi = "--UMI ${reverse[0]}" + } + } + else { + umi = '' + } + + """ + run-trust4 \\ + ${bam_mode} \\ + ${single_end_mode} \\ + ${paired_end_mode} \\ + ${barcode} \\ + ${readFormat} \\ + ${umi} \\ + -t $task.cpus \\ + -f ${fasta} \\ + -o ${prefix} \\ + ${reference} \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + trust4: \$(run-trust4 2>&1 | grep -o 'v[0-9.]*-r[0-9]*' | sed 's/^/TRUST4 using /' ) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_airr.tsv + touch ${prefix}_airr_align.tsv + touch ${prefix}_report.tsv + touch ${prefix}_assembled_reads.fa + touch ${prefix}_annot.fa + touch ${prefix}_cdr3.out + touch ${prefix}_raw.out + touch ${prefix}_final.out + touch ${prefix}_toassemble.fq + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + trust4: \$(run-trust4 2>&1 | grep -o 'v[0-9.]*-r[0-9]*' | sed 's/^/TRUST4 using /' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/trust4/meta.yml b/modules/nf-core/trust4/meta.yml new file mode 100644 index 00000000..da2a5ff4 --- /dev/null +++ b/modules/nf-core/trust4/meta.yml @@ -0,0 +1,151 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "trust4" +description: Run TRUST4 on RNA-seq data +keywords: + - sort + - example + - genomics +tools: + - "trust4": + description: "TCR and BCR assembly from bulk or single-cell RNA-seq data" + homepage: "https://github.com/liulab-dfci/TRUST4" + documentation: "https://github.com/liulab-dfci/TRUST4" + tool_dev_url: "https://github.com/liulab-dfci/TRUST4" + licence: ["GPL v3"] + identifier: biotools:trust4 + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: BAM file from bulk or single-cell RNA-seq data + pattern: "*.bam" + - reads: + type: file + description: List of input FastQ files of size 1 and 2 for single-end and paired-end + data, respectively + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Path to the fasta file coordinate and sequence of V/D/J/C genes + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vdj_reference: + type: file + description: reference file of V/D/J genes + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - barcode_read: + type: file + description: barcode read file + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - umi_read: + type: file + description: umi read file +output: + - tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: tsv files created by TRUST4 + pattern: "*.tsv" + - airr_files: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_airr.tsv": + type: file + description: TRUST4 results in AIRR format + pattern: "*_airr.tsv" + - airr_tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}_airr.tsv: + type: file + description: TRUST4 results in AIRR format + pattern: "*_airr.tsv" + - report_tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_report.tsv": + type: file + description: TRUST4 report in tsv format + pattern: "*_report.tsv" + - fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fa": + type: file + description: Fasta files created by TRUST4 + pattern: "*.fa" + - out: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.out": + type: file + description: Further report files + pattern: "*.out" + - fq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fq": + type: file + description: Fastq files created by TRUST4 + pattern: "*.fq" + - outs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "**": + type: file + description: outputt files + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@mapo9, @Joaodemeirelles" +maintainers: + - "@mapo9" diff --git a/modules/nf-core/trust4/tests/main.nf.test b/modules/nf-core/trust4/tests/main.nf.test new file mode 100644 index 00000000..7b6c36da --- /dev/null +++ b/modules/nf-core/trust4/tests/main.nf.test @@ -0,0 +1,123 @@ +nextflow_process { + + name "Test Process TRUST4" + script "../main.nf" + process "TRUST4" + + tag "modules" + tag "modules_nfcore" + tag "trust4" + + test("sarscov2 - single_end") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [], // bam + [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] // reads + ]) + input[1] = [[ id:'test'],[file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)]] // fasta + input[2] = [[ id:'test'],[]] // ref + input[3] = [[ id:'test'],[]] // barcode + input[4] = [[ id:'test'],[]] // umi + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.airr_tsv, + process.out.fq, + process.out.fasta, + process.out.report_tsv, + process.out.versions, + ).match() }, + { assert process.out.out[0][1][0] ==~ ".*/test_cdr3.out" }, + { assert process.out.out[0][1][1] ==~ ".*/test_final.out" }, + { assert process.out.out[0][1][2] ==~ ".*/test_raw.out" }, + { assert process.out.tsv[0][1][0] ==~ ".*/test_airr.tsv" }, + { assert process.out.tsv[0][1][1] ==~ ".*/test_airr_align.tsv" }, + { assert process.out.tsv[0][1][2] ==~ ".*/test_report.tsv" } + ) + } + + } + + test("sarscov2 - paired_end") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [], // bam + [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] // reads + ]) + input[1] = [[ id:'test'],[file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)]] // fasta + input[2] = [[ id:'test'],[]] // ref + input[3] = [[ id:'test'], null] // barcode + input[4] = [[ id:'test'], null] // umi + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.airr_tsv, + process.out.fq, + process.out.fasta, + process.out.report_tsv, + process.out.versions, + ).match() }, + { assert process.out.out[0][1][0] ==~ ".*/test_cdr3.out" }, + { assert process.out.out[0][1][1] ==~ ".*/test_final.out" }, + { assert process.out.out[0][1][2] ==~ ".*/test_raw.out" }, + { assert process.out.tsv[0][1][0] ==~ ".*/test_airr.tsv" }, + { assert process.out.tsv[0][1][1] ==~ ".*/test_airr_align.tsv" }, + { assert process.out.tsv[0][1][2] ==~ ".*/test_report.tsv" } + ) + } + + } + + test("sarscov2 - single_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [], + [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + input[1] = [[ id:'test'],[file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true)]] + input[2] = [[ id:'test'],[]] // ref + input[3] = [[ id:'test'],[]] // barcode + input[4] = [[ id:'test'],[]] // umi + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match("versions") }, + { assert process.out.out[0][1][0] ==~ ".*/test_cdr3.out" }, + { assert process.out.out[0][1][1] ==~ ".*/test_final.out" }, + { assert process.out.out[0][1][2] ==~ ".*/test_raw.out" }, + { assert process.out.tsv[0][1][0] ==~ ".*/test_airr.tsv" }, + { assert process.out.tsv[0][1][1] ==~ ".*/test_airr_align.tsv" }, + { assert process.out.tsv[0][1][2] ==~ ".*/test_report.tsv" } + ) + } + + } + +} diff --git a/modules/nf-core/trust4/tests/main.nf.test.snap b/modules/nf-core/trust4/tests/main.nf.test.snap new file mode 100644 index 00000000..75414757 --- /dev/null +++ b/modules/nf-core/trust4/tests/main.nf.test.snap @@ -0,0 +1,119 @@ +{ + "sarscov2 - single_end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": true + }, + "test_airr.tsv:md5,572c69a08a82acc5ff9a2bf95488b0a4" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test_toassemble.fq:md5,bd7ab2f9ea96290e58e868e4aabccf1f" + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + [ + "test_annot.fa:md5,4b07aefcac3763f7f3d242d9371060df", + "test_assembled_reads.fa:md5,2c9601da894105f2fe6c068659214db3" + ] + ] + ], + [ + [ + { + "id": "test", + "single_end": true + }, + "test_report.tsv:md5,51623a22f060007a69207b1ebdf3a7cd" + ] + ], + [ + "versions.yml:md5,ef2e18f5d083f09211fb613305df93e8" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T13:50:19.120375" + }, + "versions": { + "content": [ + [ + "versions.yml:md5,ef2e18f5d083f09211fb613305df93e8" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T13:48:46.513295" + }, + "sarscov2 - paired_end": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test_airr.tsv:md5,572c69a08a82acc5ff9a2bf95488b0a4" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_toassemble_1.fq:md5,bd7ab2f9ea96290e58e868e4aabccf1f", + "test_toassemble_2.fq:md5,0211588305d478e10879fb35b93e13d5" + ] + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_annot.fa:md5,4207f198195fa19b505ffa67feba776a", + "test_assembled_reads.fa:md5,60f27ccec04b5b1826ecf1fd87fd4ad6" + ] + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test_report.tsv:md5,51623a22f060007a69207b1ebdf3a7cd" + ] + ], + [ + "versions.yml:md5,ef2e18f5d083f09211fb613305df93e8" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2024-06-04T13:50:24.230727" + } +} \ No newline at end of file diff --git a/modules/nf-core/trust4/tests/tags.yml b/modules/nf-core/trust4/tests/tags.yml new file mode 100644 index 00000000..cacc72be --- /dev/null +++ b/modules/nf-core/trust4/tests/tags.yml @@ -0,0 +1,2 @@ +trust4: + - "modules/nf-core/trust4/**" diff --git a/nextflow.config b/nextflow.config index e51ff966..2955ec03 100644 --- a/nextflow.config +++ b/nextflow.config @@ -52,12 +52,15 @@ params { filterseq_q = 20 // Mask primers - primer_r1_maxerror = 0.2 primer_r2_maxerror = 0.2 - primer_mask_mode = 'cut' + primer_r1_mask_mode = 'cut' + primer_r2_mask_mode = 'cut' + maskprimers_align_race = false maskprimers_align = false - primer_extract_len = 0 + maskprimers_extract = false + primer_r1_extract_len = 0 + primer_r2_extract_len = 0 primer_maxlen = 50 // Build consensus @@ -85,7 +88,7 @@ params { reference_fasta = "${params.pipelines_testdata_base_path}database-cache/imgtdb_base.zip" fetch_imgt = false save_databases = true - isotype_column = 'c_call' + skip_alignment_filter = false // ----------------------- // bulk filtering options @@ -123,13 +126,20 @@ params { // ----------------------- reference_10x = null + // ----------------------- + // raw RNA seq input options + // ----------------------- + cell_barcode_read = null + read_format = null + umi_read = null + // ----------------------- // generic nf-core options // ----------------------- // References - igenomes_base = 's3://ngi-igenomes/igenomes' + igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = true // MultiQC options @@ -149,47 +159,26 @@ params { monochrome_logs = false hook_url = null help = false + help_full = false + show_hidden = false version = false // Config options config_profile_name = null config_profile_description = null + custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" config_profile_contact = null config_profile_url = null - // Max resource options - // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' - // Schema validation default options - validationFailUnrecognisedParams = false - validationLenientMode = false - validationSchemaIgnoreParams = 'genomes,igenomes_base' - validationShowHiddenParams = false - validate_params = true - + validate_params = true } // Load base.config by default for all pipelines includeConfig 'conf/base.config' -// Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} - -// Load nf-core/airrflow custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/airrflow.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/airrflow profiles: ${params.custom_config_base}/pipeline/airrflow.config") -} profiles { debug { dumpHashes = true @@ -204,7 +193,7 @@ profiles { podman.enabled = false shifter.enabled = false charliecloud.enabled = false - conda.channels = ['conda-forge', 'bioconda', 'defaults'] + conda.channels = ['conda-forge', 'bioconda'] apptainer.enabled = false } mamba { @@ -304,32 +293,36 @@ profiles { test_fetchimgt { includeConfig 'conf/test_fetchimgt.config' } test_10x_sc { includeConfig 'conf/test_10x_sc.config' } test_clontech_umi { includeConfig 'conf/test_clontech_umi.config' } + test_maskprimers_extract { includeConfig 'conf/test_maskprimers_extract.config' } + test_maskprimers_align {includeConfig 'conf/test_maskprimers_align.config' } test_nebnext_umi { includeConfig 'conf/test_nebnext_umi.config' } + test_rnaseq_bulk { includeConfig 'conf/test_rnaseq_bulk.config' } + test_rnaseq_sc { includeConfig 'conf/test_rnaseq_sc.config' } nebnext_umi_tcr { includeConfig 'conf/nebnext_umi_tcr.config' } nebnext_umi_bcr { includeConfig 'conf/nebnext_umi_bcr.config' } clontech_umi_bcr { includeConfig 'conf/clontech_umi_bcr.config' } clontech_umi_tcr { includeConfig 'conf/clontech_umi_tcr.config' } } -// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile -// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled -// Set to your registry if you have a mirror of containers -apptainer.registry = 'quay.io' -docker.registry = 'quay.io' -podman.registry = 'quay.io' -singularity.registry = 'quay.io' +// Load nf-core custom profiles from different Institutions +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" -// Nextflow plugins -plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet -} +// Load nf-core/airrflow custom profiles from different institutions. +// Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs +// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/airrflow.config" : "/dev/null" + +// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile +// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled +// Set to your registry if you have a mirror of containers +apptainer.registry = 'quay.io' +docker.registry = 'quay.io' +podman.registry = 'quay.io' +singularity.registry = 'quay.io' +charliecloud.registry = 'quay.io' // Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} +includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config' + // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -343,8 +336,15 @@ env { JULIA_DEPOT_PATH = "/usr/local/share/julia" } -// Capture exit codes from upstream processes when piping -process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Set bash options +process.shell = """\ +bash + +set -e # Exit if a tool returns a non-zero status/exit code +set -u # Treat unset variables and parameters as an error +set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute +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 @@ -369,47 +369,50 @@ dag { manifest { name = 'nf-core/airrflow' - author = """Gisela Gabernet, Susanna Marquez, Alexander Peltzer, Simon Heumos""" + author = """Gisela Gabernet, Susanna Marquez, Alexander Peltzer""" homePage = 'https://github.com/nf-core/airrflow' description = """B and T cell repertoire analysis pipeline with the Immcantation framework.""" mainScript = 'main.nf' - nextflowVersion = '!>=23.04.0' - version = '4.1.0' - doi = '10.5281/zenodo.2642009' + nextflowVersion = '!>=24.04.2' + version = '4.2.0' + doi = 'https://doi.org/10.1371/journal.pcbi.1012265' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' +// Nextflow plugins +plugins { + id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet +} -// Function to ensure that resource requirements don't go beyond -// a maximum limit -def check_max(obj, type) { - if (type == 'memory') { - try { - if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) - return params.max_memory as nextflow.util.MemoryUnit - else - return obj - } catch (all) { - println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'time') { - try { - if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) - return params.max_time as nextflow.util.Duration - else - return obj - } catch (all) { - println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" - return obj - } - } else if (type == 'cpus') { - try { - return Math.min( obj, params.max_cpus as int ) - } catch (all) { - println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" - return obj - } +validation { + defaultIgnoreParams = ["genomes"] + help { + enabled = true + command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + fullParameter = "help_full" + showHiddenParameter = "show_hidden" + beforeText = """ +-\033[2m----------------------------------------------------\033[0m- + \033[0;32m,--.\033[0;30m/\033[0;32m,-.\033[0m +\033[0;34m ___ __ __ __ ___ \033[0;32m/,-._.--~\'\033[0m +\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} ${manifest.version}\033[0m +-\033[2m----------------------------------------------------\033[0m- +""" + afterText = """${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 +""" + } + summary { + beforeText = validation.help.beforeText + afterText = validation.help.afterText } } + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index 1c32a276..aeac4cad 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,12 +1,12 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/nf-core/airrflow/master/nextflow_schema.json", "title": "nf-core/airrflow pipeline parameters", "description": "B and T cell repertoire analysis pipeline with the Immcantation framework.", "type": "object", - "definitions": { + "$defs": { "input_output_options": { - "title": "Input/output options", + "title": "Input output options", "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", @@ -61,7 +61,14 @@ "type": "string", "fa_icon": "fas fa-flask", "description": "Protocol used for the V(D)J amplicon sequencing library generation.", - "enum": ["specific_pcr_umi", "specific_pcr", "dt_5p_race", "dt_5p_race_umi", "sc_10x_genomics"], + "enum": [ + "specific_pcr_umi", + "specific_pcr", + "dt_5p_race", + "dt_5p_race_umi", + "sc_10x_genomics", + "trust4" + ], "help_text": "Available protocols are:\n- `specific_pcr_umi`: RT-PCR using transcript-specific primers containing UMIs.\n- `specific_pcr`: RT-PCR using transcript-specific primers.\n- `dt_5p_race_umi`: 5\u2019-RACE PCR using oligo-dT primers and template switch primers containing UMI.\n- `dt_5p_race`: 5\u2019-RACE PCR (i.e. RT is followed by a template switch (TS) step) using oligo-dT primers.\n- `sc_10x_genomics`:10x genomics library preparation protocol for scVDJ sequencing." }, "race_linker": { @@ -72,8 +79,8 @@ }, "fa_icon": "fas fa-flask" }, - "primer_handling": { - "title": "Primer handling", + "primer_input_and_positions": { + "title": "Primer input and positions", "type": "object", "description": "Define the primer region start and how to deal with the primer alignment.", "default": "", @@ -207,7 +214,7 @@ } }, "sequence_assembly_options": { - "title": "sequence assembly options", + "title": "Sequence Assembly options", "type": "object", "description": "Options for the pRESTO sequence assembly processes", "default": "", @@ -224,14 +231,6 @@ "description": "Maximum error for building the primer consensus in the pRESTO Buildconsensus step.", "fa_icon": "fas fa-align-left" }, - "primer_mask_mode": { - "type": "string", - "default": "cut", - "description": "Masking mode for the pRESTO MaskPrimer step. Available: cut, mask, trim, tag.", - "enum": ["cut", "mask", "tag", "trim"], - "help_text": "The primer masking modes will perform the following actions:\n\n* `cut`: remove both the primer region and the preceding sequence.\n* `mask`: replace the primer region with Ns and remove the preceding sequence.\n* `trim`: remove the region preceding the primer, but leave the primer region intact.\n* `tag`: leave the input sequence unmodified.", - "fa_icon": "fas fa-mask" - }, "buildconsensus_maxerror": { "type": "number", "default": 0.1, @@ -267,18 +266,52 @@ "fa_icon": "fas fa-align-center", "description": "Align primers instead of scoring them. Used for protocols without primer fixed positions." }, - "primer_extract_len": { - "type": "integer", - "default": 0, - "fa_icon": "fas fa-align-center", - "description": "Length of the extracted primers with MaskPrimer extract." - }, "primer_maxlen": { "type": "integer", "default": 50, "fa_icon": "fas fa-align-center", "description": "Maximum allowed primer length when aligning the primers." }, + "primer_r1_mask_mode": { + "type": "string", + "fa_icon": "fas fa-mask", + "description": "Masking mode for R1 primers.", + "enum": ["cut", "mask", "trim", "tag"], + "default": "cut", + "help_text": "See [pRESTO MaskPrimers](https://presto.readthedocs.io/en/stable/tools/MaskPrimers.html) for more information." + }, + "primer_r2_mask_mode": { + "type": "string", + "default": "cut", + "fa_icon": "fas fa-mask", + "enum": ["cut", "mask", "trim", "tag"], + "description": "Masking mode for R2 primers.", + "help_text": "See [pRESTO MaskPrimers](https://presto.readthedocs.io/en/stable/tools/MaskPrimers.html) for more information." + }, + "maskprimers_align_race": { + "type": "boolean", + "fa_icon": "fas fa-align-center", + "description": "Use MaskPrimers align for a 5' RACE protocol.", + "help_text": "It will align the C-primers with pRESTO MaskPrimers align, and extract the template-switch Oligo and/or linker with defined length in `--primer_r2_extract_len`." + }, + "maskprimers_extract": { + "type": "boolean", + "fa_icon": "fas fa-cut", + "description": "Use when primer sequences are unknown but when their approximate positions are known.", + "help_text": "Use in combination with `--primer_r1_extract_len` and `--primer_r2_extract_len` to define the sequence regions to cut corresponding to the approximate unknown primer sequence length prior to alignment. It is also possible to define a UMI barcode for extraction if it's position is unknown." + }, + "primer_r1_extract_len": { + "type": "integer", + "default": 0, + "fa_icon": "fas fa-cut", + "description": "R1 primer extract length when using `--maskprimers_extract`." + }, + "primer_r2_extract_len": { + "type": "integer", + "default": 0, + "fa_icon": "fas fa-cut", + "description": "R2 primer extract length when using `--maskprimers_extract`." + }, "assemblepairs_sequential": { "type": "boolean", "fa_icon": "fas fa-align-center", @@ -311,6 +344,11 @@ "default": "tag", "fa_icon": "fas fa-mask", "description": "Mask mode for C-region alignment." + }, + "skip_alignment_filter": { + "type": "boolean", + "fa_icon": "fas fa-fast-forward", + "description": "Skip filter step after alignment that ensures that locus should match the v_call chain, the sequence alignment should have at least 200 informative positions (excluding N or gaps), and maximum 10% N nucleotides in the alignment." } }, "fa_icon": "fas fa-align-center" @@ -336,31 +374,27 @@ "save_databases": { "type": "boolean", "description": "Save databases so you can use the cache in future runs.", - "fa_icon": "fas fa-file-download" + "fa_icon": "fas fa-file-download", + "default": true }, "reference_fasta": { "type": "string", "description": "Path to the germline reference fasta.", "help_text": "By default, we provide a pre-downloaded version of the IMGT database. It is also possible to provide a custom reference fasta database. To fetch a fresh version of IMGT, set the `--fetch_imgt` parameter instead.", - "fa_icon": "fas fa-database" + "fa_icon": "fas fa-database", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip" }, "reference_igblast": { "type": "string", "description": "Path to the cached igblast database.", "help_text": "By default, we provide a pre-downloaded version of the IMGT database. It is also possible to provide a custom reference fasta database. To fetch a fresh version of IMGT, set the `--fetch_imgt` parameter instead.", - "fa_icon": "fas fa-database" + "fa_icon": "fas fa-database", + "default": "https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip" }, "fetch_imgt": { "type": "boolean", "description": "Set this flag to fetch the IMGT reference data at runtime.", "fa_icon": "fas fa-cloud-download-alt" - }, - "isotype_column": { - "type": "string", - "description": "Set the column in the AIRR rearrangement file that isotype information should be gathered from.", - "default": "c_call", - "fa_icon": "fas fa-border-all", - "help_text": "Default is the `c_call` column. For bulk protocols one can use the c_primers or cregion columns (check `align_cregion`). The primer or cregions fasta file header need to contain the strings `IGHA`, `IGHD`, `IGHG`... for the isotypes to be properly parsed. This will be used for plotting mutation frequency by isotype in the clonal analysis report." } }, "fa_icon": "fas fa-edit" @@ -434,13 +468,13 @@ "default": "raxml", "description": "Lineage tree software to use to build trees within Dowser. If you change the default, also set the `lineage_tree_exec` parameter.", "enum": ["raxml", "igphyml"], - "fa_icon": "fas fa-pagelines" + "fa_icon": "fab fa-pagelines" }, "lineage_tree_exec": { "type": "string", "default": "/usr/local/bin/raxml-ng", "description": "Path to lineage tree building executable.", - "fa_icon": "fas fa-pagelines" + "fa_icon": "fab fa-pagelines" }, "singlecell": { "type": "string", @@ -478,6 +512,36 @@ "help_text": "Options for running raw single cell data.", "fa_icon": "fab fa-pagelines" }, + "rnaseq_based_analysis_options": { + "title": "Unselected RNA-seq based analysis options", + "type": "object", + "description": "Options specific for raw unselected RNA-seq input.", + "default": "", + "properties": { + "cell_barcode_read": { + "type": "string", + "description": "Specifies which read holds the barcodes", + "enum": ["R1", "R2"], + "fa_icon": "fas fa-terminal", + "help_text": "file containing the barcodes" + }, + "umi_read": { + "type": "string", + "description": "Indicate if UMI indices are recorded in the R1 (default) or R1 fastq file.", + "help_text": "file containing 10x Genomics-like UMIs", + "enum": ["R1", "R2"], + "fa_icon": "fas fa-barcode" + }, + "read_format": { + "type": "string", + "description": "Specifies where in the read the barcodes and UMIs can be found.", + "help_text": "For further information see the TRUST4 [docs](https://github.com/liulab-dfci/TRUST4?tab=readme-ov-file#10x-genomics-data-and-barcode-based-single-cell-data).", + "fa_icon": "fas fa-terminal" + } + }, + "help_text": "Options for running raw RNA seq data.", + "fa_icon": "fab fa-pagelines" + }, "report_options": { "title": "Report options", "type": "object", @@ -527,14 +591,6 @@ "fa_icon": "fas fa-dna", "description": "Options for the reference genome indices used to align reads.", "properties": { - "igenomes_base": { - "type": "string", - "format": "directory-path", - "description": "Directory / URL base for iGenomes references.", - "default": "s3://ngi-igenomes/igenomes", - "fa_icon": "fas fa-cloud-download-alt", - "hidden": true - }, "igenomes_ignore": { "type": "boolean", "description": "Do not load the iGenomes reference config.", @@ -542,6 +598,14 @@ "hidden": true, "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.", "default": true + }, + "igenomes_base": { + "type": "string", + "format": "directory-path", + "description": "The base path to the igenomes reference files", + "fa_icon": "fas fa-ban", + "hidden": true, + "default": "s3://ngi-igenomes/igenomes/" } } }, @@ -594,41 +658,6 @@ } } }, - "max_job_request_options": { - "title": "Max job request options", - "type": "object", - "fa_icon": "fas fa-microchip", - "description": "Set the top limit for requested resources for any single job.", - "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", - "properties": { - "max_cpus": { - "type": "integer", - "description": "Maximum number of CPUs that can be requested for any single job.", - "default": 16, - "fa_icon": "fas fa-microchip", - "hidden": true, - "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" - }, - "max_memory": { - "type": "string", - "description": "Maximum amount of memory that can be requested for any single job.", - "default": "128.GB", - "fa_icon": "fas fa-memory", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "hidden": true, - "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" - }, - "max_time": { - "type": "string", - "description": "Maximum amount of time that can be requested for any single job.", - "default": "240.h", - "fa_icon": "far fa-clock", - "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$", - "hidden": true, - "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" - } - } - }, "generic_options": { "title": "Generic options", "type": "object", @@ -636,12 +665,6 @@ "description": "Less common options for the pipeline, typically set in a config file.", "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", "properties": { - "help": { - "type": "boolean", - "description": "Display help text.", - "fa_icon": "fas fa-question-circle", - "hidden": true - }, "version": { "type": "boolean", "description": "Display version and exit.", @@ -722,27 +745,6 @@ "fa_icon": "fas fa-check-square", "hidden": true }, - "validationShowHiddenParams": { - "type": "boolean", - "fa_icon": "far fa-eye-slash", - "description": "Show all params when using `--help`", - "hidden": true, - "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." - }, - "validationFailUnrecognisedParams": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters fails when an unrecognised parameter is found.", - "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." - }, - "validationLenientMode": { - "type": "boolean", - "fa_icon": "far fa-check-circle", - "description": "Validation of parameters in lenient more.", - "hidden": true, - "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)." - }, "pipelines_testdata_base_path": { "type": "string", "fa_icon": "far fa-check-circle", @@ -755,49 +757,82 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" + }, + { + "$ref": "#/$defs/protocol" + }, + { + "$ref": "#/$defs/primer_input_and_positions" + }, + { + "$ref": "#/$defs/umi_barcode_handling" + }, + { + "$ref": "#/$defs/adapter_trimming" + }, + { + "$ref": "#/$defs/sequence_assembly_options" + }, + { + "$ref": "#/$defs/vdj_annotation_options" + }, + { + "$ref": "#/$defs/bulk_filtering_options" + }, + { + "$ref": "#/$defs/clonal_analysis_options" + }, + { + "$ref": "#/$defs/single_cell_analysis_options" + }, + { + "$ref": "#/$defs/rnaseq_based_analysis_options" + }, + { + "$ref": "#/$defs/report_options" }, { - "$ref": "#/definitions/protocol" + "$ref": "#/$defs/protocol" }, { - "$ref": "#/definitions/primer_handling" + "$ref": "#/$defs/primer_input_and_positions" }, { - "$ref": "#/definitions/umi_barcode_handling" + "$ref": "#/$defs/umi_barcode_handling" }, { - "$ref": "#/definitions/adapter_trimming" + "$ref": "#/$defs/adapter_trimming" }, { - "$ref": "#/definitions/sequence_assembly_options" + "$ref": "#/$defs/sequence_assembly_options" }, { - "$ref": "#/definitions/vdj_annotation_options" + "$ref": "#/$defs/vdj_annotation_options" }, { - "$ref": "#/definitions/bulk_filtering_options" + "$ref": "#/$defs/bulk_filtering_options" }, { - "$ref": "#/definitions/clonal_analysis_options" + "$ref": "#/$defs/clonal_analysis_options" }, { - "$ref": "#/definitions/report_options" + "$ref": "#/$defs/single_cell_analysis_options" }, { - "$ref": "#/definitions/reference_genome_options" + "$ref": "#/$defs/rnaseq_based_analysis_options" }, { - "$ref": "#/definitions/single_cell_analysis_options" + "$ref": "#/$defs/report_options" }, { - "$ref": "#/definitions/institutional_config_options" + "$ref": "#/$defs/reference_genome_options" }, { - "$ref": "#/definitions/max_job_request_options" + "$ref": "#/$defs/institutional_config_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/local/fastq_input_check.nf b/subworkflows/local/fastq_input_check.nf index e14cfc21..91412b15 100644 --- a/subworkflows/local/fastq_input_check.nf +++ b/subworkflows/local/fastq_input_check.nf @@ -29,8 +29,8 @@ workflow FASTQ_INPUT_CHECK { ch_versions = SAMPLESHEET_CHECK.out.versions - // Merge multi-lane sample fastq for protocols except for 10x genomics (cellranger handles multi-fastq per sample) - if (params.library_generation_method == 'sc_10x_genomics') { + // Merge multi-lane sample fastq for protocols except for 10x genomics, trust4 (cellranger handles multi-fastq per sample) + if (params.library_generation_method == 'sc_10x_genomics' || params.library_generation_method == 'trust4') { ch_merged_reads = ch_reads.single.mix( ch_reads.multiple ) @@ -85,10 +85,9 @@ def create_fastq_channels(LinkedHashMap col) { } array = [ meta, [ file(col.filename_R1), file(col.filename_R2), file(col.filename_I1) ] ] } else { - array = [ meta, [ file(col.filename_R1), file(col.filename_R2) ] ] if (params.index_file) { - error "ERROR: --index_file was provided but the index file path is not specified in the samplesheet!" + error "ERROR: Index file path was provided but the index file path is not specified in the samplesheet!" } } return array diff --git a/subworkflows/local/presto_sans_umi.nf b/subworkflows/local/presto_sans_umi.nf index 8d75856d..0161d769 100644 --- a/subworkflows/local/presto_sans_umi.nf +++ b/subworkflows/local/presto_sans_umi.nf @@ -7,11 +7,14 @@ include { FASTP } from '../../modu //PRESTO include { PRESTO_ASSEMBLEPAIRS as PRESTO_ASSEMBLEPAIRS_SANS_UMI } from '../../modules/local/presto/presto_assemblepairs' include { PRESTO_FILTERSEQ_POSTASSEMBLY as PRESTO_FILTERSEQ_POSTASSEMBLY_SANS_UMI } from '../../modules/local/presto/presto_filterseq_postassembly' -include { PRESTO_MASKPRIMERS_POSTASSEMBLY as PRESTO_MASKPRIMERS_POSTASSEMBLY_SANS_UMI } from '../../modules/local/presto/presto_maskprimers_postassembly' -include { PRESTO_PARSEHEADERS_PRIMERS as PRESTO_PARSEHEADERS_PRIMERS_SANS_UMI } from '../../modules/local/presto/presto_parseheaders_primers' -include { PRESTO_PARSEHEADERS_METADATA as PRESTO_PARSEHEADERS_METADATA_SANS_UMI } from '../../modules/local/presto/presto_parseheaders_metadata' -include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_SANS_UMI } from '../../modules/local/presto/presto_collapseseq' -include { PRESTO_SPLITSEQ as PRESTO_SPLITSEQ_SANS_UMI} from '../../modules/local/presto/presto_splitseq' +include { PRESTO_MASKPRIMERS_SCORE as PRESTO_MASKPRIMERS_SCORE_SANSUMI_FWD } from '../../modules/local/presto/presto_maskprimers_score' +include { PRESTO_MASKPRIMERS_SCORE as PRESTO_MASKPRIMERS_SCORE_SANSUMI_REV } from '../../modules/local/presto/presto_maskprimers_score' +include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_MASKPRIMERS_ALIGN_SANSUMI_FWD } from '../../modules/local/presto/presto_maskprimers_align' +include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_MASKPRIMERS_ALIGN_SANSUMI_REV } from '../../modules/local/presto/presto_maskprimers_align' +include { PRESTO_PARSEHEADERS_PRIMERS as PRESTO_PARSEHEADERS_PRIMERS_SANS_UMI } from '../../modules/local/presto/presto_parseheaders_primers' +include { PRESTO_PARSEHEADERS_METADATA as PRESTO_PARSEHEADERS_METADATA_SANS_UMI } from '../../modules/local/presto/presto_parseheaders_metadata' +include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_SANS_UMI } from '../../modules/local/presto/presto_collapseseq' +include { PRESTO_SPLITSEQ as PRESTO_SPLITSEQ_SANS_UMI} from '../../modules/local/presto/presto_splitseq' workflow PRESTO_SANS_UMI { @@ -54,22 +57,128 @@ workflow PRESTO_SANS_UMI { ch_versions = ch_versions.mix(PRESTO_FILTERSEQ_POSTASSEMBLY_SANS_UMI.out.versions) // Mask primers - PRESTO_MASKPRIMERS_POSTASSEMBLY_SANS_UMI ( - PRESTO_FILTERSEQ_POSTASSEMBLY_SANS_UMI.out.reads, - ch_cprimers.collect(), - ch_vprimers.collect() - ) - ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_POSTASSEMBLY_SANS_UMI.out.versions) + def suffix_FWD = "R1" + def suffix_REV = "R2" + def barcode_R1 = false + def barcode_R2 = false + ch_reads = PRESTO_FILTERSEQ_POSTASSEMBLY_SANS_UMI.out.reads + if (params.maskprimers_align){ + if (params.cprimer_position == "R1") { + PRESTO_MASKPRIMERS_ALIGN_SANSUMI_FWD( + ch_reads, + ch_cprimers.collect(), + params.primer_maxlen, + params.primer_r1_maxerror, + params.primer_r1_mask_mode, + suffix_FWD + ) + PRESTO_MASKPRIMERS_ALIGN_SANSUMI_REV( + PRESTO_MASKPRIMERS_ALIGN_SANSUMI_FWD.out.reads, + ch_vprimers.collect(), + params.primer_maxlen, + params.primer_r2_maxerror, + params.primer_r2_mask_mode, + suffix_REV + ) + } else if (params.cprimer_position == "R2") { + PRESTO_MASKPRIMERS_ALIGN_SANSUMI_FWD( + ch_reads, + ch_vprimers.collect(), + params.primer_maxlen, + params.primer_r1_maxerror, + params.primer_r1_mask_mode, + suffix_FWD + ) + PRESTO_MASKPRIMERS_ALIGN_SANSUMI_REV( + PRESTO_MASKPRIMERS_ALIGN_SANSUMI_FWD.out.reads, + ch_cprimers.collect(), + params.primer_maxlen, + params.primer_r2_maxerror, + params.primer_r2_mask_mode, + suffix_REV + ) + } else { + error "Error in determining cprimer position. Please choose R1 or R2." + } + + ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_ALIGN_SANSUMI_FWD.out.versions) + + ch_maskprimers_logs = PRESTO_MASKPRIMERS_ALIGN_SANSUMI_FWD.out.logs + ch_maskprimers_logs = ch_maskprimers_logs.mix(PRESTO_MASKPRIMERS_ALIGN_SANSUMI_REV.out.logs) + + ch_masked_reads = PRESTO_MASKPRIMERS_ALIGN_SANSUMI_REV.out.reads + } else { + if (params.cprimer_position == "R1") { + def start_FWD = "${params.cprimer_start}" + def start_REV = "${params.vprimer_start}" + def revpr_FWD = false + PRESTO_MASKPRIMERS_SCORE_SANSUMI_FWD( + ch_reads, + ch_cprimers.collect(), + start_FWD, + barcode_R1, + params.primer_r1_maxerror, + params.primer_r1_mask_mode, + revpr_FWD, + suffix_FWD + ) + PRESTO_MASKPRIMERS_SCORE_SANSUMI_REV( + PRESTO_MASKPRIMERS_SCORE_SANSUMI_FWD.out.reads, + ch_vprimers.collect(), + start_REV, + barcode_R2, + params.primer_r2_maxerror, + params.primer_r2_mask_mode, + params.primer_revpr, + suffix_REV + ) + } else if (params.cprimer_position == "R2") { + def start_FWD = "${params.vprimer_start}" + def start_REV = "${params.cprimer_start}" + def revpr_FWD = false + + PRESTO_MASKPRIMERS_SCORE_SANSUMI_FWD( + ch_reads, + ch_vprimers.collect(), + start_FWD, + barcode_R1, + params.primer_r1_maxerror, + params.primer_r1_mask_mode, + revpr_FWD, + suffix_FWD + ) + PRESTO_MASKPRIMERS_SCORE_SANSUMI_REV( + PRESTO_MASKPRIMERS_SCORE_SANSUMI_FWD.out.reads, + ch_cprimers.collect(), + start_REV, + barcode_R2, + params.primer_r2_maxerror, + params.primer_r2_mask_mode, + params.primer_revpr, + suffix_REV + ) + } else { + error "Error in determining cprimer position. Please choose R1 or R2." + } + + ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_SCORE_SANSUMI_FWD.out.versions) + + ch_maskprimers_logs = PRESTO_MASKPRIMERS_SCORE_SANSUMI_FWD.out.logs + ch_maskprimers_logs = ch_maskprimers_logs.mix(PRESTO_MASKPRIMERS_SCORE_SANSUMI_REV.out.logs) + + ch_masked_reads = PRESTO_MASKPRIMERS_SCORE_SANSUMI_REV.out.reads + + } // Generate QC stats after reads paired and filtered but before collapsed FASTQC_POSTASSEMBLY_SANS_UMI ( - PRESTO_MASKPRIMERS_POSTASSEMBLY_SANS_UMI.out.reads + ch_masked_reads ) ch_versions = ch_versions.mix(FASTQC_POSTASSEMBLY_SANS_UMI.out.versions) // Annotate primers in C_PRIMER and V_PRIMER field PRESTO_PARSEHEADERS_PRIMERS_SANS_UMI ( - PRESTO_MASKPRIMERS_POSTASSEMBLY_SANS_UMI.out.reads + ch_masked_reads ) ch_versions = ch_versions.mix(PRESTO_PARSEHEADERS_PRIMERS_SANS_UMI.out.versions) @@ -99,7 +208,7 @@ workflow PRESTO_SANS_UMI { fastqc_postassembly_gz = FASTQC_POSTASSEMBLY_SANS_UMI.out.zip presto_assemblepairs_logs = PRESTO_ASSEMBLEPAIRS_SANS_UMI.out.logs.collect() presto_filterseq_logs = PRESTO_FILTERSEQ_POSTASSEMBLY_SANS_UMI.out.logs - presto_maskprimers_logs = PRESTO_MASKPRIMERS_POSTASSEMBLY_SANS_UMI.out.logs.collect() + presto_maskprimers_logs = ch_maskprimers_logs.collect() presto_collapseseq_logs = PRESTO_COLLAPSESEQ_SANS_UMI.out.logs.collect() presto_splitseq_logs = PRESTO_SPLITSEQ_SANS_UMI.out.logs.collect() } diff --git a/subworkflows/local/presto_umi.nf b/subworkflows/local/presto_umi.nf index 17caa68e..3034d236 100644 --- a/subworkflows/local/presto_umi.nf +++ b/subworkflows/local/presto_umi.nf @@ -7,28 +7,37 @@ include { FASTP } from '../../modules/n //PRESTO -include { PRESTO_FILTERSEQ as PRESTO_FILTERSEQ_UMI } from '../../modules/local/presto/presto_filterseq' -include { PRESTO_MASKPRIMERS as PRESTO_MASKPRIMERS_UMI } from '../../modules/local/presto/presto_maskprimers' -include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_ALIGN_PRIMERS } from '../../modules/local/presto/presto_maskprimers_align' -include { PRESTO_MASKPRIMERS_EXTRACT } from '../../modules/local/presto/presto_maskprimers_extract' -include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_ALIGN_CREGION } from '../../modules/local/presto/presto_maskprimers_align' -include { PRESTO_PAIRSEQ as PRESTO_PAIRSEQ_UMI } from '../../modules/local/presto/presto_pairseq' -include { PRESTO_PAIRSEQ as PRESTO_PAIRSEQ_ALIGN } from '../../modules/local/presto/presto_pairseq' -include { PRESTO_CLUSTERSETS as PRESTO_CLUSTERSETS_UMI } from '../../modules/local/presto/presto_clustersets' -include { PRESTO_PARSE_CLUSTER as PRESTO_PARSE_CLUSTER_UMI } from '../../modules/local/presto/presto_parse_cluster' -include { PRESTO_BUILDCONSENSUS as PRESTO_BUILDCONSENSUS_UMI} from '../../modules/local/presto/presto_buildconsensus' -include { PRESTO_BUILDCONSENSUS as PRESTO_BUILDCONSENSUS_ALIGN } from '../../modules/local/presto/presto_buildconsensus' +include { PRESTO_FILTERSEQ as PRESTO_FILTERSEQ_UMI } from '../../modules/local/presto/presto_filterseq' +include { PRESTO_MASKPRIMERS as PRESTO_MASKPRIMERS_UMI } from '../../modules/local/presto/presto_maskprimers' +include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_ALIGN_PRIMERS } from '../../modules/local/presto/presto_maskprimers_align' +include { PRESTO_MASKPRIMERS_EXTRACT as PRESTO_MASKPRIMERS_EXTRACT } from '../../modules/local/presto/presto_maskprimers_extract' +include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_ALIGN_CREGION } from '../../modules/local/presto/presto_maskprimers_align' +include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_MASKPRIMERS_ALIGN_UMI_R1 } from '../../modules/local/presto/presto_maskprimers_align' +include { PRESTO_MASKPRIMERS_ALIGN as PRESTO_MASKPRIMERS_ALIGN_UMI_R2 } from '../../modules/local/presto/presto_maskprimers_align' +include { PRESTO_MASKPRIMERS_SCORE as PRESTO_MASKPRIMERS_SCORE_UMI_R1 } from '../../modules/local/presto/presto_maskprimers_score' +include { PRESTO_MASKPRIMERS_SCORE as PRESTO_MASKPRIMERS_SCORE_UMI_R2 } from '../../modules/local/presto/presto_maskprimers_score' +include { PRESTO_MASKPRIMERS_EXTRACT as PRESTO_MASKPRIMERS_EXTRACT_R1 } from '../../modules/local/presto/presto_maskprimers_extract' +include { PRESTO_MASKPRIMERS_EXTRACT as PRESTO_MASKPRIMERS_EXTRACT_R2 } from '../../modules/local/presto/presto_maskprimers_extract' +include { PRESTO_PAIRSEQ as PRESTO_PAIRSEQ_UMI } from '../../modules/local/presto/presto_pairseq' +include { PRESTO_PAIRSEQ as PRESTO_PAIRSEQ_ALIGN } from '../../modules/local/presto/presto_pairseq' +include { PRESTO_PAIRSEQ as PRESTO_PAIRSEQ_EXTRACT } from '../../modules/local/presto/presto_pairseq' +include { PRESTO_PAIRSEQ as PRESTO_PAIRSEQ_CLUSTERSETS } from '../../modules/local/presto/presto_pairseq' +include { PRESTO_CLUSTERSETS as PRESTO_CLUSTERSETS_UMI } from '../../modules/local/presto/presto_clustersets' +include { PRESTO_PARSE_CLUSTER as PRESTO_PARSE_CLUSTER_UMI } from '../../modules/local/presto/presto_parse_cluster' +include { PRESTO_BUILDCONSENSUS as PRESTO_BUILDCONSENSUS_UMI } from '../../modules/local/presto/presto_buildconsensus' +include { PRESTO_BUILDCONSENSUS as PRESTO_BUILDCONSENSUS_ALIGN_RACE } from '../../modules/local/presto/presto_buildconsensus' +include { PRESTO_BUILDCONSENSUS as PRESTO_BUILDCONSENSUS_EXTRACT } from '../../modules/local/presto/presto_buildconsensus' include { PRESTO_POSTCONSENSUS_PAIRSEQ as PRESTO_POSTCONSENSUS_PAIRSEQ_UMI } from '../../modules/local/presto/presto_postconsensus_pairseq' -include { PRESTO_ASSEMBLEPAIRS as PRESTO_ASSEMBLEPAIRS_UMI } from '../../modules/local/presto/presto_assemblepairs' -include { PRESTO_ASSEMBLEPAIRS_SEQUENTIAL } from '../../modules/local/presto/presto_assemblepairs_sequential' -include { PRESTO_PARSEHEADERS as PRESTO_PARSEHEADERS_COLLAPSE_UMI } from '../../modules/local/presto/presto_parseheaders' -include { PRESTO_PARSEHEADERS as PRESTO_PARSEHEADERS_CREGION } from '../../modules/local/presto/presto_parseheaders' -include { PRESTO_PARSEHEADERS_PRIMERS as PRESTO_PARSEHEADERS_PRIMERS_UMI } from '../../modules/local/presto/presto_parseheaders_primers' +include { PRESTO_ASSEMBLEPAIRS as PRESTO_ASSEMBLEPAIRS_UMI } from '../../modules/local/presto/presto_assemblepairs' +include { PRESTO_ASSEMBLEPAIRS_SEQUENTIAL } from '../../modules/local/presto/presto_assemblepairs_sequential' +include { PRESTO_PARSEHEADERS as PRESTO_PARSEHEADERS_COLLAPSE_UMI } from '../../modules/local/presto/presto_parseheaders' +include { PRESTO_PARSEHEADERS as PRESTO_PARSEHEADERS_CREGION } from '../../modules/local/presto/presto_parseheaders' +include { PRESTO_PARSEHEADERS_PRIMERS as PRESTO_PARSEHEADERS_PRIMERS_UMI } from '../../modules/local/presto/presto_parseheaders_primers' include { PRESTO_PARSEHEADERS_METADATA as PRESTO_PARSEHEADERS_METADATA_UMI } from '../../modules/local/presto/presto_parseheaders_metadata' -include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_UMI } from '../../modules/local/presto/presto_collapseseq' -include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_ALIGN } from '../../modules/local/presto/presto_collapseseq' -include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_CREGION} from '../../modules/local/presto/presto_collapseseq' -include { PRESTO_SPLITSEQ as PRESTO_SPLITSEQ_UMI } from '../../modules/local/presto/presto_splitseq' +include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_UMI } from '../../modules/local/presto/presto_collapseseq' +include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_ALIGN } from '../../modules/local/presto/presto_collapseseq' +include { PRESTO_COLLAPSESEQ as PRESTO_COLLAPSESEQ_CREGION } from '../../modules/local/presto/presto_collapseseq' +include { PRESTO_SPLITSEQ as PRESTO_SPLITSEQ_UMI } from '../../modules/local/presto/presto_splitseq' workflow PRESTO_UMI { @@ -44,6 +53,11 @@ workflow PRESTO_UMI { ch_versions = Channel.empty() + // Validate params + if (params.maskprimers_align_race & params.umi_position == 'R1') {error "The maskprimers align race option is only supported with UMI barcodes in the R2 reads (reads containing V region)."} + if (params.maskprimers_align_race & params.cprimer_position == 'R2') {error "The maskprimers align race option is only supported with Cprimers in the R1 reads (reads containing C region)."} + + // Merge UMI from index file to R1 if provided if (params.index_file) { @@ -101,22 +115,33 @@ workflow PRESTO_UMI { PRESTO_FILTERSEQ_UMI ( GUNZIP_UMI.out.reads ) ch_versions = ch_versions.mix(PRESTO_FILTERSEQ_UMI.out.versions) + // Split reads into R1 and R2 + ch_reads_R1 = PRESTO_FILTERSEQ_UMI.out.reads + .map{ reads -> [reads[0], reads[1]] }.dump(tag: 'ch_reads_R1') + ch_reads_R2 = PRESTO_FILTERSEQ_UMI.out.reads + .map{ reads -> [reads[0], reads[2]] }.dump(tag: 'ch_reads_R2') + // Mask primers - if (params.maskprimers_align) { + if (params.maskprimers_align_race) { - ch_reads_R1 = PRESTO_FILTERSEQ_UMI.out.reads - .map{ reads -> [reads[0], reads[1]] }.dump(tag: 'ch_reads_R1') - ch_reads_R2 = PRESTO_FILTERSEQ_UMI.out.reads - .map{ reads -> [reads[0], reads[2]] }.dump(tag: 'ch_reads_R2') PRESTO_ALIGN_PRIMERS( ch_reads_R1, ch_cprimers.collect(), params.primer_maxlen, + false, params.primer_r1_maxerror, - params.primer_mask_mode + params.primer_r1_mask_mode, + false, + "R1" ) + PRESTO_MASKPRIMERS_EXTRACT( - ch_reads_R2 + ch_reads_R2, + params.umi_length, + params.primer_r2_extract_len, + params.primer_r2_mask_mode, + true, + "R2" ) ch_versions = ch_versions.mix(PRESTO_ALIGN_PRIMERS.out.versions) @@ -130,25 +155,249 @@ workflow PRESTO_UMI { ch_maskprimers_logs = PRESTO_ALIGN_PRIMERS.out.logs ch_maskprimers_logs = ch_maskprimers_logs.mix(PRESTO_MASKPRIMERS_EXTRACT.out.logs) - PRESTO_PAIRSEQ_ALIGN( ch_maskprimers_reads ) + def barcode_position = (params.umi_position == "R1" | params.index_file) ? "R1" : "R2" + + PRESTO_PAIRSEQ_ALIGN( + ch_maskprimers_reads, + barcode_position + ) ch_versions = ch_versions.mix(PRESTO_PAIRSEQ_ALIGN.out.versions) ch_for_clustersets = PRESTO_PAIRSEQ_ALIGN.out.reads ch_pairseq_logs = PRESTO_PAIRSEQ_ALIGN.out.logs - } else { + } else if (params.maskprimers_align) { - PRESTO_MASKPRIMERS_UMI ( - PRESTO_FILTERSEQ_UMI.out.reads, - ch_cprimers.collect(), - ch_vprimers.collect() + if (params.cprimer_position == "R1") { + def barcode_R1 = (params.index_file | params.umi_position == 'R1') ? true : false + + PRESTO_MASKPRIMERS_ALIGN_UMI_R1( + ch_reads_R1, + ch_cprimers.collect(), + params.primer_maxlen, + barcode_R1, + params.primer_r1_maxerror, + params.primer_r1_mask_mode, + false, + "R1" + ) + + def barcode_R2 = (params.umi_position == "R2") ? true : false + + PRESTO_MASKPRIMERS_ALIGN_UMI_R2( + ch_reads_R2, + ch_vprimers.collect(), + params.primer_maxlen, + barcode_R2, + params.primer_r2_maxerror, + params.primer_r2_mask_mode, + params.primer_revpr, + "R2" + ) + } else if (params.cprimer_position == "R2") { + def barcode_R1 = (params.index_file | params.umi_position == 'R1') ? true : false + + PRESTO_MASKPRIMERS_ALIGN_UMI_R1( + ch_reads_R1, + ch_vprimers.collect(), + params.primer_maxlen, + barcode_R1, + params.primer_r1_maxerror, + params.primer_r1_mask_mode, + false, + "R1" + ) + def barcode_R2 = (params.umi_position == "R2") ? true : false + + PRESTO_MASKPRIMERS_ALIGN_UMI_R2( + ch_reads_R2, + ch_cprimers.collect(), + params.primer_maxlen, + barcode_R2, + params.primer_r2_maxerror, + params.primer_r2_mask_mode, + params.primer_revpr, + "R2" + ) + } else { + error "Error in determining cprimer position. Please choose R1 or R2." + } + + ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_ALIGN_UMI_R1.out.versions) + ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_ALIGN_UMI_R2.out.versions) + + // Merge again R1 and R2 by sample ID. + ch_maskprimers_reads_R1 = PRESTO_MASKPRIMERS_ALIGN_UMI_R1.out.reads.map{ reads -> [reads[0].id, reads[0], reads[1]]}.dump(tag: 'ch_maskprimers_reads_R1') + ch_maskprimers_reads_R2 = PRESTO_MASKPRIMERS_ALIGN_UMI_R2.out.reads.map{ reads -> [reads[0].id, reads[0], reads[1]]}.dump(tag: 'ch_maskprimers_reads_R2') + ch_maskprimers_reads = ch_maskprimers_reads_R1.join(ch_maskprimers_reads_R2) + .map{ it -> [it[1], it[2], it[4]] }.dump(tag: 'ch_maskprimers_reads_after_remerge') + + ch_maskprimers_logs = PRESTO_MASKPRIMERS_ALIGN_UMI_R1.out.logs + ch_maskprimers_logs = ch_maskprimers_logs.mix(PRESTO_MASKPRIMERS_ALIGN_UMI_R2.out.logs) + + // Pre-consensus pair + def barcode_position = (params.umi_position == "R1" | params.index_file) ? "R1" : "R2" + + PRESTO_PAIRSEQ_UMI ( + ch_maskprimers_reads, + barcode_position + ) + + ch_versions = ch_versions.mix(PRESTO_PAIRSEQ_UMI.out.versions) + ch_for_clustersets = PRESTO_PAIRSEQ_UMI.out.reads + ch_pairseq_logs = PRESTO_PAIRSEQ_UMI.out.logs + + } else if (params.maskprimers_extract){ + + if (params.cprimer_position == "R1"){ + def barcode_R1 = (params.index_file | params.umi_position == 'R1') ? true : false + def cprimer_start = (params.index_file | params.umi_position == 'R1') ? "${params.umi_length + params.cprimer_start}" : "${params.cprimer_start}" + + PRESTO_MASKPRIMERS_EXTRACT_R1( + ch_reads_R1, + cprimer_start, + params.primer_r1_extract_len, + params.primer_r1_mask_mode, + barcode_R1, + "R1" + ) + + def barcode_R2 = (params.umi_position == "R2") ? true : false + def vprimer_start = (params.umi_position == "R2") ? "${params.umi_length + params.vprimer_start}" : "${params.vprimer_start}" + + PRESTO_MASKPRIMERS_EXTRACT_R2( + ch_reads_R2, + vprimer_start, + params.primer_r2_extract_len, + params.primer_r2_mask_mode, + barcode_R2, + "R2" + ) + } else if (params.cprimer_position == "R2") { + def barcode_R1 = (params.index_file | params.umi_position == 'R1') ? true : false + def vprimer_start = (params.index_file | params.umi_position == 'R1') ? "${params.umi_length + params.vprimer_start}" : "${params.vprimer_start}" + + PRESTO_MASKPRIMERS_EXTRACT_R1( + ch_reads_R1, + vprimer_start, + params.primer_r1_extract_len, + params.primer_r1_mask_mode, + barcode_R1, + "R1" + ) + + def barcode_R2 = (params.umi_position == "R2") ? true : false + def cprimer_start = (params.umi_position == "R2") ? "${params.umi_length + params.cprimer_start}" : "${params.cprimer_start}" + + PRESTO_MASKPRIMERS_EXTRACT_R2( + ch_reads_R2, + cprimer_start, + params.primer_r2_extract_len, + params.primer_r2_mask_mode, + barcode_R2, + "R2" + ) + } else { + error "Error in determining cprimer position. Please choose R1 or R2." + } + + ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_EXTRACT_R1.out.versions) + ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_EXTRACT_R2.out.versions) + + // Merge again R1 and R2 by sample ID. + ch_maskprimers_reads_R1 = PRESTO_MASKPRIMERS_EXTRACT_R1.out.reads.map{ reads -> [reads[0].id, reads[0], reads[1]]}.dump(tag: 'ch_maskprimers_reads_R1') + ch_maskprimers_reads_R2 = PRESTO_MASKPRIMERS_EXTRACT_R2.out.reads.map{ reads -> [reads[0].id, reads[0], reads[1]]}.dump(tag: 'ch_maskprimers_reads_R2') + ch_maskprimers_reads = ch_maskprimers_reads_R1.join(ch_maskprimers_reads_R2) + .map{ it -> [it[1], it[2], it[4]] }.dump(tag: 'ch_maskprimers_reads_after_remerge') + + ch_maskprimers_logs = PRESTO_MASKPRIMERS_EXTRACT_R1.out.logs + ch_maskprimers_logs = ch_maskprimers_logs.mix(PRESTO_MASKPRIMERS_EXTRACT_R2.out.logs) + + def barcode_position = (params.umi_position == "R1" | params.index_file) ? "R1" : "R2" + PRESTO_PAIRSEQ_EXTRACT( + ch_maskprimers_reads, + barcode_position ) - ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_UMI.out.versions) - ch_maskprimers_logs = PRESTO_MASKPRIMERS_UMI.out.logs + ch_versions = ch_versions.mix(PRESTO_PAIRSEQ_EXTRACT.out.versions) + ch_for_clustersets = PRESTO_PAIRSEQ_EXTRACT.out.reads + ch_pairseq_logs = PRESTO_PAIRSEQ_EXTRACT.out.logs + + } else { + + if (params.cprimer_position == "R1") { + def barcode_R1 = (params.index_file | params.umi_position == 'R1') ? true : false + def cprimer_start = (params.index_file | params.umi_position == 'R1') ? "${params.umi_length + params.cprimer_start}" : "${params.cprimer_start}" + PRESTO_MASKPRIMERS_SCORE_UMI_R1( + ch_reads_R1, + ch_cprimers.collect(), + cprimer_start, + barcode_R1, + params.primer_r1_maxerror, + params.primer_r1_mask_mode, + false, + "R1" + ) + + def barcode_R2 = (params.umi_position == "R2") ? true : false + def vprimer_start = (params.umi_position == "R2") ? "${params.umi_length + params.vprimer_start}" : "${params.vprimer_start}" + PRESTO_MASKPRIMERS_SCORE_UMI_R2( + ch_reads_R2, + ch_vprimers.collect(), + vprimer_start, + barcode_R2, + params.primer_r2_maxerror, + params.primer_r2_mask_mode, + params.primer_revpr, + "R2" + ) + } else if (params.cprimer_position == "R2") { + def barcode_R1 = (params.index_file | params.umi_position == 'R1') ? true : false + def vprimer_start = (params.index_file | params.umi_position == 'R1') ? "${params.umi_length + params.vprimer_start}" : "${params.vprimer_start}" + PRESTO_MASKPRIMERS_SCORE_UMI_R1( + ch_reads_R1, + ch_vprimers.collect(), + vprimer_start, + barcode_R1, + params.primer_r1_maxerror, + params.primer_r1_mask_mode, + revpr_R1, + "R1" + ) + def barcode_R2 = (params.umi_position == "R2") ? true : false + def cprimer_start = (params.umi_position == "R2") ? "${params.umi_length + params.cprimer_start}" : "${params.cprimer_start}" + + PRESTO_MASKPRIMERS_SCORE_UMI_R2( + ch_reads_R2, + ch_cprimers.collect(), + cprimer_start, + barcode_R2, + params.primer_r2_maxerror, + params.primer_r2_mask_mode, + params.primer_revpr, + "R2" + ) + } else { + error "Error in determining cprimer position. Please choose R1 or R2." + } + + ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_SCORE_UMI_R1.out.versions) + ch_versions = ch_versions.mix(PRESTO_MASKPRIMERS_SCORE_UMI_R2.out.versions) + + // Merge again R1 and R2 by sample ID. + ch_maskprimers_reads_R1 = PRESTO_MASKPRIMERS_SCORE_UMI_R1.out.reads.map{ reads -> [reads[0].id, reads[0], reads[1]]}.dump(tag: 'ch_maskprimers_reads_R1') + ch_maskprimers_reads_R2 = PRESTO_MASKPRIMERS_SCORE_UMI_R2.out.reads.map{ reads -> [reads[0].id, reads[0], reads[1]]}.dump(tag: 'ch_maskprimers_reads_R2') + ch_maskprimers_reads = ch_maskprimers_reads_R1.join(ch_maskprimers_reads_R2) + .map{ it -> [it[1], it[2], it[4]] }.dump(tag: 'ch_maskprimers_reads_after_remerge') + + ch_maskprimers_logs = PRESTO_MASKPRIMERS_SCORE_UMI_R1.out.logs + ch_maskprimers_logs = ch_maskprimers_logs.mix(PRESTO_MASKPRIMERS_SCORE_UMI_R2.out.logs) // Pre-consensus pair + def barcode_position = (params.umi_position == "R1" | params.index_file) ? "R1" : "R2" PRESTO_PAIRSEQ_UMI ( - PRESTO_MASKPRIMERS_UMI.out.reads + ch_maskprimers_reads, + barcode_position ) + ch_versions = ch_versions.mix(PRESTO_PAIRSEQ_UMI.out.versions) ch_for_clustersets = PRESTO_PAIRSEQ_UMI.out.reads ch_pairseq_logs = PRESTO_PAIRSEQ_UMI.out.logs @@ -168,23 +417,41 @@ workflow PRESTO_UMI { PRESTO_CLUSTERSETS_UMI.out.reads ) ch_versions = ch_versions.mix(PRESTO_PARSE_CLUSTER_UMI.out.versions) - ch_for_buildconsensus = PRESTO_PARSE_CLUSTER_UMI.out.reads ch_clustersets_logs = PRESTO_CLUSTERSETS_UMI.out.logs.collect() + // Combining the split cluster+UMI combination + PRESTO_PAIRSEQ_CLUSTERSETS ( + PRESTO_PARSE_CLUSTER_UMI.out.reads, + "clustersets" + ) + ch_versions = ch_versions.mix(PRESTO_PAIRSEQ_CLUSTERSETS.out.versions) + + ch_for_buildconsensus = PRESTO_PAIRSEQ_CLUSTERSETS.out.reads + } else { ch_for_buildconsensus = ch_for_clustersets ch_clustersets_logs = Channel.empty() } // Build consensus of sequences with same UMI barcode - if (params.maskprimers_align) { - PRESTO_BUILDCONSENSUS_ALIGN ( + if (params.maskprimers_align_race) { + // Only consider C_PRIMER frequency when building consensus + PRESTO_BUILDCONSENSUS_ALIGN_RACE ( + ch_for_buildconsensus + ) + ch_versions = ch_versions.mix(PRESTO_BUILDCONSENSUS_ALIGN_RACE.out.versions) + ch_postconsensus = PRESTO_BUILDCONSENSUS_ALIGN_RACE.out.reads + ch_buildconsensus_logs = PRESTO_BUILDCONSENSUS_ALIGN_RACE.out.logs + } else if (params.maskprimers_extract) { + // Do not consider primers when building consensus + PRESTO_BUILDCONSENSUS_EXTRACT( ch_for_buildconsensus ) - ch_versions = ch_versions.mix(PRESTO_BUILDCONSENSUS_ALIGN.out.versions) - ch_postconsensus = PRESTO_BUILDCONSENSUS_ALIGN.out.reads - ch_buildconsensus_logs = PRESTO_BUILDCONSENSUS_ALIGN.out.logs + ch_versions = ch_versions.mix(PRESTO_BUILDCONSENSUS_EXTRACT.out.versions) + ch_postconsensus = PRESTO_BUILDCONSENSUS_EXTRACT.out.reads + ch_buildconsensus_logs = PRESTO_BUILDCONSENSUS_EXTRACT.out.logs } else { + // Consider both primers frequency when building consensus PRESTO_BUILDCONSENSUS_UMI ( ch_for_buildconsensus ) @@ -224,8 +491,11 @@ workflow PRESTO_UMI { ch_assemblepairs_reads, ch_internal_cregion.collect(), params.cregion_maxlen, + false, params.cregion_maxerror, - params.cregion_mask_mode + params.cregion_mask_mode, + false, + "Cregion" ) ch_parseheaders_reads = PRESTO_ALIGN_CREGION.out.reads ch_versions = ch_versions.mix(PRESTO_ALIGN_CREGION.out.versions) @@ -246,7 +516,8 @@ workflow PRESTO_UMI { ch_versions = ch_versions.mix(PRESTO_PARSEHEADERS_COLLAPSE_UMI.out.versions) // Annotate primer fields and collapse duplicates - if (params.maskprimers_align) { + if (params.maskprimers_align_race) { + // Rename primer field to CREGION PRESTO_PARSEHEADERS_CREGION ( PRESTO_PARSEHEADERS_COLLAPSE_UMI.out.reads @@ -261,7 +532,18 @@ workflow PRESTO_UMI { ch_collapsed = PRESTO_COLLAPSESEQ_ALIGN.out.reads ch_collapse_logs = PRESTO_COLLAPSESEQ_ALIGN.out.logs + } else if (params.maskprimers_extract) { + + // Do not annotate primers + PRESTO_COLLAPSESEQ_UMI ( + PRESTO_PARSEHEADERS_COLLAPSE_UMI.out.reads + ) + ch_versions = ch_versions.mix(PRESTO_COLLAPSESEQ_UMI.out.versions) + ch_collapsed = PRESTO_COLLAPSESEQ_UMI.out.reads + ch_collapse_logs = PRESTO_COLLAPSESEQ_UMI.out.logs + } else { + // Annotate primers in C_PRIMER and V_PRIMER field PRESTO_PARSEHEADERS_PRIMERS_UMI ( PRESTO_PARSEHEADERS_COLLAPSE_UMI.out.reads diff --git a/subworkflows/local/repertoire_analysis_reporting.nf b/subworkflows/local/repertoire_analysis_reporting.nf index 2a796751..905c2d85 100644 --- a/subworkflows/local/repertoire_analysis_reporting.nf +++ b/subworkflows/local/repertoire_analysis_reporting.nf @@ -30,7 +30,7 @@ workflow REPERTOIRE_ANALYSIS_REPORTING { main: ch_versions = Channel.empty() - if (params.mode == "fastq" && params.library_generation_method != "sc_10x_genomics") { + if (params.mode == "fastq" && params.library_generation_method != "sc_10x_genomics" && params.library_generation_method != "trust4" ) { PARSE_LOGS( ch_presto_filterseq_logs, ch_presto_maskprimers_logs, diff --git a/subworkflows/local/rnaseq_input.nf b/subworkflows/local/rnaseq_input.nf new file mode 100644 index 00000000..9c42fc2e --- /dev/null +++ b/subworkflows/local/rnaseq_input.nf @@ -0,0 +1,136 @@ +include { PREPARE_TRUST4_REFERENCE } from '../../modules/local/prepare_trust4_reference' +include { TRUST4 } from '../../modules/nf-core/trust4/main' +include { FASTQ_INPUT_CHECK } from '../../subworkflows/local/fastq_input_check' +include { CHANGEO_PARSEDB_SELECT_LOCUS } from '../../modules/local/changeo/changeo_parsedb_select_locus' +include { CHANGEO_CONVERTDB_FASTA as CHANGEO_CONVERTDB_FASTA_FROM_AIRR } from '../../modules/local/changeo/changeo_convertdb_fasta' +include { FASTP } from '../../modules/nf-core/fastp/main' +include { RENAME_FASTQ as RENAME_FASTQ_TRUST4 } from '../../modules/local/rename_fastq' + + + +workflow RNASEQ_INPUT { + + take: + ch_input + ch_igblast_reference + + main: + + ch_versions = Channel.empty() + ch_logs = Channel.empty() + + // + // read in samplesheet, validate and stage input fies + // + FASTQ_INPUT_CHECK( + ch_input + ) + ch_versions = ch_versions.mix(FASTQ_INPUT_CHECK.out.versions) + + ch_reads = FASTQ_INPUT_CHECK.out.reads + + + // validate library generation method parameters + if (params.vprimers) { + error "The TRUST4 library generation method does not require V-region primers, please provide a reference file instead or select another library method option." + } else if (params.race_linker) { + error "The TRUST4 10X genomics library generation method does not require the --race_linker parameter, please provide a reference file instead or select another library method option." + } + if (params.cprimers) { + error "The TRUST4 library generation method does not require C-region primers, please provide a reference file instead or select another library method option." + } + if (params.umi_length > 0) { + error "TRUST4 library generation method does not require to set the UMI length, please provide a reference file instead or select another library method option." + } + if (params.reference_10x) { + error "The TRUST4 library generation method does not require this reference, please provide a compliant reference file instead or select another library method option." + } + + // Fastp + save_merged = false + FASTP ( + ch_reads, + [], + [], + save_merged + ) + ch_versions = ch_versions.mix(FASTP.out.versions) + + ch_rename_fastq = FASTP.out.reads.map { meta, reads -> [meta, reads[0], reads[1]] } + + // rename fastp output + RENAME_FASTQ_TRUST4( + ch_rename_fastq + ) + + ch_reads_fastp_filtered = RENAME_FASTQ_TRUST4.out.reads.dump(tag: "fastp_filtered") + + PREPARE_TRUST4_REFERENCE( + ch_reads_fastp_filtered.first(), + ch_igblast_reference + ) + + + // create trust4 input + ch_reads_trust4 = ch_reads_fastp_filtered.map{ meta, read_1, read_2 -> [ meta, [], [read_1, read_2] ] } + + PREPARE_TRUST4_REFERENCE.out.trust4_reference.dump(tag: "trust4_reference") + + ch_reads_trust4.dump(tag: "trust4_input") + + // create barcode and umi channels for nf-core trust4 module + barcode_channel = ch_reads_fastp_filtered.map { meta, read_1, read_2 -> [meta, params.cell_barcode_read] } + umi_channel = ch_reads_fastp_filtered.map { meta, read_1, read_2 -> [meta, params.umi_read] } + ch_reference_trust4 = PREPARE_TRUST4_REFERENCE.out.trust4_reference.map { reference -> [[id: "igblast_reference"], reference] } + + TRUST4( + ch_reads_trust4, + ch_reference_trust4.collect(), + Channel.of([[], []]).collect(), + barcode_channel, + umi_channel + ) + + ch_trust4_out = TRUST4.out.outs + + // check whether input is sc or bulk and extract respective airr file for downstream processing + ch_trust4_out + .branch { + meta, out_files -> + bulk : meta["single_cell"] == "false" + return [ meta, out_files.find { it.endsWith("${meta.id}_airr.tsv") } ] + sc : meta["single_cell"] == "true" + return [ meta, out_files.find { it.endsWith("${meta.id}_barcode_airr.tsv") } ] + } + .set { ch_trust4_airr_file } + + + // create channel with airr file + ch_trust4_airr_file.bulk.mix ( ch_trust4_airr_file.sc ).set { ch_trust4_airr } + + // select only provided locus + CHANGEO_PARSEDB_SELECT_LOCUS(ch_trust4_airr) + + + // convert airr tsv to fasta + CHANGEO_CONVERTDB_FASTA_FROM_AIRR( + CHANGEO_PARSEDB_SELECT_LOCUS.out.tab + ) + + ch_fasta = CHANGEO_CONVERTDB_FASTA_FROM_AIRR.out.fasta + + + emit: + versions = ch_versions + // fastp + fastp_reads_json = FASTP.out.json.collect{ meta,json -> json } + fastp_reads_html = FASTP.out.html.collect{ meta,html -> html } + // complete trust4 output + outs = ch_trust4_out + // trust4 airr file + airr = ch_trust4_airr + // trust4 output converted to FASTA format + fasta = ch_fasta + samplesheet = FASTQ_INPUT_CHECK.out.samplesheet + +} diff --git a/subworkflows/local/sequence_assembly.nf b/subworkflows/local/sequence_assembly.nf index d001b124..f7248463 100644 --- a/subworkflows/local/sequence_assembly.nf +++ b/subworkflows/local/sequence_assembly.nf @@ -67,18 +67,23 @@ workflow SEQUENCE_ASSEMBLY { // Validate library generation method parameter if (params.library_generation_method == 'specific_pcr_umi'){ - if (params.vprimers) { - ch_vprimers_fasta = Channel.fromPath(params.vprimers, checkIfExists: true) + if (!params.maskprimers_extract){ + if (params.vprimers) { + ch_vprimers_fasta = Channel.fromPath(params.vprimers, checkIfExists: true) + } else { + error "Please provide a V-region primers fasta file with the '--vprimers' option when using the 'specific_pcr_umi' library generation method." + } + if (params.cprimers) { + ch_cprimers_fasta = Channel.fromPath(params.cprimers, checkIfExists: true) + } else { + error "Please provide a C-region primers fasta file with the '--cprimers' option when using the 'specific_pcr_umi' library generation method." + } + if (params.race_linker) { + error "Please do not set '--race_linker' when using the 'specific_pcr_umi' library generation method." + } } else { - error "Please provide a V-region primers fasta file with the '--vprimers' option when using the 'specific_pcr_umi' library generation method." - } - if (params.cprimers) { - ch_cprimers_fasta = Channel.fromPath(params.cprimers, checkIfExists: true) - } else { - error "Please provide a C-region primers fasta file with the '--cprimers' option when using the 'specific_pcr_umi' library generation method." - } - if (params.race_linker) { - error "Please do not set '--race_linker' when using the 'specific_pcr_umi' library generation method." + ch_vprimers_fasta = Channel.of([]) + ch_cprimers_fasta = Channel.of([]) } if (params.umi_length < 2) { error "The 'specific_pcr_umi' library generation method requires setting the '--umi_length' to a value greater than 1." @@ -115,7 +120,7 @@ workflow SEQUENCE_ASSEMBLY { error "The oligo-dT 5'-RACE UMI library generation method does not accept V-region primers, please provide a linker with '--race_linker' instead or select another library method option." } else if (params.race_linker) { ch_vprimers_fasta = Channel.fromPath(params.race_linker, checkIfExists: true) - } else if (params.maskprimers_align) { + } else if (params.maskprimers_align_race) { ch_vprimers_fasta = Channel.of([]) } else { error "The oligo-dT 5'-RACE UMI library generation method requires a linker or Template Switch Oligo sequence, please provide it with the option '--race_linker'." @@ -138,7 +143,7 @@ workflow SEQUENCE_ASSEMBLY { error "The oligo-dT 5'-RACE library generation method does not accept V-region primers, please provide a linker with '--race_linker' instead or select another library method option." } else if (params.race_linker) { ch_vprimers_fasta = Channel.fromPath(params.race_linker, checkIfExists: true) - } else if (params.maskprimers_align) { + } else if (params.maskprimers_align_race) { ch_vprimers_fasta = Channel.of([]) } else { error "The oligo-dT 5'-RACE library generation method requires a linker or Template Switch Oligo sequence, please provide it with the option '--race_linker'." @@ -164,8 +169,6 @@ workflow SEQUENCE_ASSEMBLY { if (params.index_file & params.umi_position == 'R2') {error "Please do not set `--umi_position` option if index file with UMIs is provided."} if (params.umi_length < 0) {error "Please provide the UMI barcode length in the option `--umi_length`. To run without UMIs, set umi_length to 0."} if (!params.index_file & params.umi_start != 0) {error "Setting a UMI start position is only allowed when providing the UMIs in a separate index read file. If so, please provide the `--index_file` flag as well."} - if (params.maskprimers_align & params.umi_position == 'R1') {error "The maskprimers align option is only supported with UMI barcodes in the R2 reads (reads containing V region)."} - if (params.maskprimers_align & params.cprimer_position == 'R2') {error "The maskprimers align option is only supported with Cprimers in the R1 reads (reads containing C region)."} // // SUBWORKFLOW: Read in samplesheet, validate and stage input files diff --git a/subworkflows/local/utils_nfcore_airrflow_pipeline/main.nf b/subworkflows/local/utils_nfcore_airrflow_pipeline/main.nf index ebbb9e90..d3760821 100644 --- a/subworkflows/local/utils_nfcore_airrflow_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_airrflow_pipeline/main.nf @@ -8,29 +8,25 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { UTILS_NFVALIDATION_PLUGIN } from '../../nf-core/utils_nfvalidation_plugin' -include { paramsSummaryMap } from 'plugin/nf-validation' -include { fromSamplesheet } from 'plugin/nf-validation' -include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' +include { UTILS_NFSCHEMA_PLUGIN } from '../../nf-core/utils_nfschema_plugin' +include { paramsSummaryMap } from 'plugin/nf-schema' +include { samplesheetToList } from 'plugin/nf-schema' include { completionEmail } from '../../nf-core/utils_nfcore_pipeline' include { completionSummary } from '../../nf-core/utils_nfcore_pipeline' -include { dashedLine } from '../../nf-core/utils_nfcore_pipeline' -include { nfCoreLogo } from '../../nf-core/utils_nfcore_pipeline' include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' -include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' +include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW TO INITIALISE PIPELINE -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_INITIALISATION { take: version // boolean: Display version and exit - help // boolean: Display help text validate_params // boolean: Boolean whether to validate parameters against the schema at runtime monochrome_logs // boolean: Do not use coloured log outputs nextflow_cli_args // array: List of positional nextflow CLI args @@ -54,16 +50,10 @@ workflow PIPELINE_INITIALISATION { // // Validate parameters and generate parameter summary to stdout // - pre_help_text = nfCoreLogo(monochrome_logs) - post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs) - def String workflow_command = "nextflow run ${workflow.manifest.name} -profile --input samplesheet.csv --outdir " - UTILS_NFVALIDATION_PLUGIN ( - help, - workflow_command, - pre_help_text, - post_help_text, + UTILS_NFSCHEMA_PLUGIN ( + workflow, validate_params, - "nextflow_schema.json" + null ) // @@ -72,6 +62,7 @@ workflow PIPELINE_INITIALISATION { UTILS_NFCORE_PIPELINE ( nextflow_cli_args ) + // // Custom validation for pipeline parameters // @@ -80,7 +71,9 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // - ch_samplesheet = Channel.fromPath(input, checkIfExists: true) + Channel.fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json")) + + Channel.fromPath(input).set{ch_samplesheet} emit: samplesheet = ch_samplesheet @@ -88,9 +81,9 @@ workflow PIPELINE_INITIALISATION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW FOR PIPELINE COMPLETION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow PIPELINE_COMPLETION { @@ -105,7 +98,6 @@ workflow PIPELINE_COMPLETION { multiqc_report // string: Path to MultiQC report main: - summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") // @@ -113,11 +105,18 @@ workflow PIPELINE_COMPLETION { // workflow.onComplete { if (email || email_on_fail) { - completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs, multiqc_report.toList()) + completionEmail( + summary_params, + email, + email_on_fail, + plaintext_email, + outdir, + monochrome_logs, + multiqc_report.toList() + ) } completionSummary(monochrome_logs) - if (hook_url) { imNotification(summary_params, hook_url) } @@ -129,9 +128,9 @@ workflow PIPELINE_COMPLETION { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Check and validate pipeline parameters @@ -147,7 +146,7 @@ def validateInputSamplesheet(input) { def (metas, fastqs) = input[1..2] // Check that multiple runs of the same sample are of the same datatype i.e. single-end / paired-end - def endedness_ok = metas.collect{ it.single_end }.unique().size == 1 + def endedness_ok = metas.collect{ meta -> meta.single_end }.unique().size == 1 if (!endedness_ok) { error("Please check input samplesheet -> Multiple runs of a sample must be of the same datatype i.e. single-end or paired-end: ${metas[0].id}") } @@ -179,7 +178,6 @@ def genomeExistsError() { error(error_string) } } - // // Generate methods description for MultiQC // @@ -239,8 +237,10 @@ def methodsDescriptionText(mqc_methods_yaml) { // 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 def temp_doi_ref = "" - String[] manifest_doi = meta.manifest_map.doi.tokenize(",") - for (String doi_ref: manifest_doi) temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + def manifest_doi = meta.manifest_map.doi.tokenize(",") + manifest_doi.each { doi_ref -> + temp_doi_ref += "(doi: ${doi_ref.replace("https://doi.org/", "").replace(" ", "")}), " + } meta["doi_text"] = temp_doi_ref.substring(0, temp_doi_ref.length() - 2) } else meta["doi_text"] = "" meta["nodoi_text"] = meta.manifest_map.doi ? "" : "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " @@ -261,3 +261,4 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } + diff --git a/subworkflows/local/vdj_annotation.nf b/subworkflows/local/vdj_annotation.nf index 692320ec..d15920a1 100644 --- a/subworkflows/local/vdj_annotation.nf +++ b/subworkflows/local/vdj_annotation.nf @@ -38,19 +38,24 @@ workflow VDJ_ANNOTATION { ch_assigned_tab = CHANGEO_MAKEDB.out.tab ch_assignment_logs = CHANGEO_MAKEDB.out.logs - // Apply quality filters: - // - locus should match v_call chain - // - seq alignment min length informative positions 200 - // - max 10% N nucleotides - FILTER_QUALITY( - ch_assigned_tab - ) - ch_logs = ch_logs.mix(FILTER_QUALITY.out.logs) - ch_versions = ch_versions.mix(FILTER_QUALITY.out.versions) + if (!params.skip_alignment_filter){ + // Apply quality filters: + // - locus should match v_call chain + // - seq alignment min length informative positions 200 + // - max 10% N nucleotides + FILTER_QUALITY( + ch_assigned_tab + ) + ch_for_parsedb_split = FILTER_QUALITY.out.tab + ch_logs = ch_logs.mix(FILTER_QUALITY.out.logs) + ch_versions = ch_versions.mix(FILTER_QUALITY.out.versions) + } else { + ch_for_parsedb_split = ch_assigned_tab + } if (params.productive_only) { CHANGEO_PARSEDB_SPLIT ( - FILTER_QUALITY.out.tab + ch_for_parsedb_split ) ch_logs = ch_logs.mix(CHANGEO_PARSEDB_SPLIT.out.logs) ch_versions = ch_versions.mix(CHANGEO_PARSEDB_SPLIT.out.versions) diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index ac31f28f..0fcbf7b3 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -2,18 +2,13 @@ // Subworkflow with functionality that may be useful for any Nextflow pipeline // -import org.yaml.snakeyaml.Yaml -import groovy.json.JsonOutput -import nextflow.extension.FilesEx - /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { - take: print_version // boolean: print version dump_parameters // boolean: dump parameters @@ -26,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Print workflow version and exit on --version // if (print_version) { - log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") System.exit(0) } @@ -49,16 +44,16 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Generate version string // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -76,13 +71,13 @@ def getWorkflowVersion() { // Dump pipeline parameters to a JSON file // def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = JsonOutput.toJson(params) - temp_pf.text = JsonOutput.prettyPrint(jsonStr) + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) - FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") + nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() } @@ -90,37 +85,40 @@ def dumpParametersToJSON(outdir) { // When running with -profile conda, warn if channels have not been set-up appropriately // def checkCondaChannels() { - Yaml parser = new Yaml() + def parser = new org.yaml.snakeyaml.Yaml() def channels = [] try { def config = parser.load("conda config --show channels".execute().text) channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return + } + catch (NullPointerException e) { + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.warn("Could not verify conda channel configuration.") + return null } // Check that all channels are present // This channel list is ordered by required channel priority. - def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] + def required_channels_in_order = ['conda-forge', 'bioconda'] def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - def n = required_channels_in_order.size() - for (int i = 0; i < n - 1; i++) { - channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config index d0a926bf..a09572e5 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config @@ -3,7 +3,7 @@ manifest { author = """nf-core""" homePage = 'https://127.0.0.1' description = """Dummy pipeline""" - nextflowVersion = '!>=23.04.0' + nextflowVersion = '!>=23.04.0' version = '9.9.9' doi = 'https://doi.org/10.5281/zenodo.5070524' } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 14558c39..5cb7bafe 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -2,17 +2,13 @@ // Subworkflow with utility functions specific to the nf-core pipeline template // -import org.yaml.snakeyaml.Yaml -import nextflow.extension.FilesEx - /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { - take: nextflow_cli_args @@ -25,23 +21,20 @@ workflow UTILS_NFCORE_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // // Warn if a -profile or Nextflow config has not been provided to run the pipeline // def checkConfigProvided() { - valid_config = true + def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) valid_config = false } return valid_config @@ -52,12 +45,14 @@ def checkConfigProvided() { // def checkProfileProvided(nextflow_cli_args) { if (workflow.profile.endsWith(',')) { - error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } if (nextflow_cli_args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } } @@ -66,25 +61,21 @@ def checkProfileProvided(nextflow_cli_args) { // def workflowCitation() { def temp_doi_ref = "" - String[] manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs + def manifest_doi = workflow.manifest.doi.tokenize(",") + // Handling multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list - for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${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" + 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 // def getWorkflowVersion() { - String version_string = "" + def version_string = "" as String if (workflow.manifest.version) { def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' version_string += "${prefix_v}${workflow.manifest.version}" @@ -102,8 +93,8 @@ def getWorkflowVersion() { // Get software versions for pipeline // def processVersionsFromYAML(yaml_file) { - Yaml yaml = new Yaml() - versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def yaml = new org.yaml.snakeyaml.Yaml() + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } return yaml.dumpAsMap(versions).trim() } @@ -113,8 +104,8 @@ def processVersionsFromYAML(yaml_file) { def workflowVersionToYAML() { return """ Workflow: - $workflow.manifest.name: ${getWorkflowVersion()} - Nextflow: $workflow.nextflow.version + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} """.stripIndent().trim() } @@ -122,11 +113,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions - .unique() - .map { processVersionsFromYAML(it) } - .unique() - .mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) } // @@ -134,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - for (group in summary_params.keySet()) { - def group_params = summary_params.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

    $group

    \n" - summary_section += "
    \n" - for (param in group_params.keySet()) { - summary_section += "
    $param
    ${group_params.get(param) ?: 'N/A'}
    \n" + summary_params + .keySet() + .each { group -> + def group_params = summary_params.get(group) + // This gets the parameters of that particular group + if (group_params) { + summary_section += "

    ${group}

    \n" + summary_section += "
    \n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
    ${param}
    ${group_params.get(param) ?: 'N/A'}
    \n" + } + summary_section += "
    \n" } - summary_section += "
    \n" } - } - String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" return yaml_file_text } @@ -161,7 +154,7 @@ def paramsSummaryMultiqc(summary_params) { // nf-core logo // def nfCoreLogo(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map String.format( """\n ${dashedLine(monochrome_logs)} @@ -180,7 +173,7 @@ def nfCoreLogo(monochrome_logs=true) { // Return dashed line // def dashedLine(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map return "-${colors.dim}----------------------------------------------------${colors.reset}-" } @@ -188,7 +181,7 @@ def dashedLine(monochrome_logs=true) { // ANSII colours used for terminal logging // def logColours(monochrome_logs=true) { - Map colorcodes = [:] + def colorcodes = [:] as Map // Reset / Meta colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" @@ -200,54 +193,54 @@ def logColours(monochrome_logs=true) { colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" return colorcodes } @@ -262,14 +255,15 @@ def attachMultiqcReport(multiqc_report) { 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" + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") } mqc_report = mqc_report[0] } } - } catch (all) { + } + catch (Exception all) { if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") } } return mqc_report @@ -281,26 +275,35 @@ def attachMultiqcReport(multiqc_report) { def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" } def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] misc_fields['Date Started'] = workflow.start misc_fields['Date Completed'] = workflow.complete misc_fields['Pipeline script file path'] = workflow.scriptFile misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] @@ -338,39 +341,41 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Render the sendmail template def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def 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) def sendmail_html = sendmail_template.toString() // Send the HTML e-mail - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { +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 $email_address (sendmail)-" - } catch (all) { + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception all) { // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") } } // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") output_tf.delete() } @@ -378,15 +383,17 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Print pipeline summary on completion // def completionSummary(monochrome_logs=true) { - Map colors = logColours(monochrome_logs) + def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } @@ -395,21 +402,30 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - for (group in summary_params.keySet()) { - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) { + misc_fields['repository'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['commitid'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['revision'] = workflow.revision + } + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp def msg_fields = [:] msg_fields['version'] = getWorkflowVersion() @@ -434,13 +450,13 @@ def imNotification(summary_params, hook_url) { def json_message = json_template.toString() // POST - def post = new URL(hook_url).openConnection(); + def post = new URL(hook_url).openConnection() post.setRequestMethod("POST") post.setDoOutput(true) post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); + post.getOutputStream().write(json_message.getBytes("UTF-8")) + def postRC = post.getResponseCode() + if (!postRC.equals(200)) { + log.warn(post.getErrorStream().getText()) } } diff --git a/subworkflows/nf-core/utils_nfschema_plugin/main.nf b/subworkflows/nf-core/utils_nfschema_plugin/main.nf new file mode 100644 index 00000000..4994303e --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/main.nf @@ -0,0 +1,46 @@ +// +// Subworkflow that uses the nf-schema plugin to validate parameters and render the parameter summary +// + +include { paramsSummaryLog } from 'plugin/nf-schema' +include { validateParameters } from 'plugin/nf-schema' + +workflow UTILS_NFSCHEMA_PLUGIN { + + take: + input_workflow // workflow: the workflow object used by nf-schema to get metadata from the workflow + validate_params // boolean: validate the parameters + parameters_schema // string: path to the parameters JSON schema. + // this has to be the same as the schema given to `validation.parametersSchema` + // when this input is empty it will automatically use the configured schema or + // "${projectDir}/nextflow_schema.json" as default. This input should not be empty + // for meta pipelines + + main: + + // + // Print parameter summary to stdout. This will display the parameters + // that differ from the default given in the JSON schema + // + if(parameters_schema) { + log.info paramsSummaryLog(input_workflow, parameters_schema:parameters_schema) + } else { + log.info paramsSummaryLog(input_workflow) + } + + // + // Validate the parameters using nextflow_schema.json or the schema + // given via the validation.parametersSchema configuration option + // + if(validate_params) { + if(parameters_schema) { + validateParameters(parameters_schema:parameters_schema) + } else { + validateParameters() + } + } + + emit: + dummy_emit = true +} + diff --git a/subworkflows/nf-core/utils_nfschema_plugin/meta.yml b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml new file mode 100644 index 00000000..f7d9f028 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/meta.yml @@ -0,0 +1,35 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "utils_nfschema_plugin" +description: Run nf-schema to validate parameters and create a summary of changed parameters +keywords: + - validation + - JSON schema + - plugin + - parameters + - summary +components: [] +input: + - input_workflow: + type: object + description: | + The workflow object of the used pipeline. + This object contains meta data used to create the params summary log + - validate_params: + type: boolean + description: Validate the parameters and error if invalid. + - parameters_schema: + type: string + description: | + Path to the parameters JSON schema. + This has to be the same as the schema given to the `validation.parametersSchema` config + option. When this input is empty it will automatically use the configured schema or + "${projectDir}/nextflow_schema.json" as default. The schema should not be given in this way + for meta pipelines. +output: + - dummy_emit: + type: boolean + description: Dummy emit to make nf-core subworkflows lint happy +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test new file mode 100644 index 00000000..842dc432 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/main.nf.test @@ -0,0 +1,117 @@ +nextflow_workflow { + + name "Test Subworkflow UTILS_NFSCHEMA_PLUGIN" + script "../main.nf" + workflow "UTILS_NFSCHEMA_PLUGIN" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/utils_nfschema_plugin" + tag "plugin/nf-schema" + + config "./nextflow.config" + + test("Should run nothing") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } + + test("Should run nothing - custom schema") { + + when { + + params { + test_data = '' + } + + workflow { + """ + validate_params = false + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.success } + ) + } + } + + test("Should validate params - custom schema") { + + when { + + params { + test_data = '' + outdir = 1 + } + + workflow { + """ + validate_params = true + input[0] = workflow + input[1] = validate_params + input[2] = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + """ + } + } + + then { + assertAll( + { assert workflow.failed }, + { assert workflow.stdout.any { it.contains('ERROR ~ Validation of pipeline parameters failed!') } } + ) + } + } +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config new file mode 100644 index 00000000..0907ac58 --- /dev/null +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -0,0 +1,8 @@ +plugins { + id "nf-schema@2.1.0" +} + +validation { + parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" + monochromeLogs = true +} \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json similarity index 95% rename from subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json rename to subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json index 7626c1c9..331e0d2f 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json @@ -1,10 +1,10 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft/2020-12/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "", "type": "object", - "definitions": { + "$defs": { "input_output_options": { "title": "Input/output options", "type": "object", @@ -87,10 +87,10 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/$defs/input_output_options" }, { - "$ref": "#/definitions/generic_options" + "$ref": "#/$defs/generic_options" } ] } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf deleted file mode 100644 index 2585b65d..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ /dev/null @@ -1,62 +0,0 @@ -// -// Subworkflow that uses the nf-validation plugin to render help text and parameter summary -// - -/* -======================================================================================== - IMPORT NF-VALIDATION PLUGIN -======================================================================================== -*/ - -include { paramsHelp } from 'plugin/nf-validation' -include { paramsSummaryLog } from 'plugin/nf-validation' -include { validateParameters } from 'plugin/nf-validation' - -/* -======================================================================================== - SUBWORKFLOW DEFINITION -======================================================================================== -*/ - -workflow UTILS_NFVALIDATION_PLUGIN { - - take: - print_help // boolean: print help - workflow_command // string: default commmand used to run pipeline - pre_help_text // string: string to be printed before help text and summary log - post_help_text // string: string to be printed after help text and summary log - validate_params // boolean: validate parameters - schema_filename // path: JSON schema file, null to use default value - - main: - - log.debug "Using schema file: ${schema_filename}" - - // Default values for strings - pre_help_text = pre_help_text ?: '' - post_help_text = post_help_text ?: '' - workflow_command = workflow_command ?: '' - - // - // Print help message if needed - // - if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text - System.exit(0) - } - - // - // Print parameter summary to stdout - // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text - - // - // Validate parameters relative to the parameter JSON schema - // - if (validate_params){ - validateParameters(parameters_schema: schema_filename) - } - - emit: - dummy_emit = true -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml deleted file mode 100644 index 3d4a6b04..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml +++ /dev/null @@ -1,44 +0,0 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "UTILS_NFVALIDATION_PLUGIN" -description: Use nf-validation to initiate and validate a pipeline -keywords: - - utility - - pipeline - - initialise - - validation -components: [] -input: - - print_help: - type: boolean - description: | - Print help message and exit - - workflow_command: - type: string - description: | - The command to run the workflow e.g. "nextflow run main.nf" - - pre_help_text: - type: string - description: | - Text to print before the help message - - post_help_text: - type: string - description: | - Text to print after the help message - - validate_params: - type: boolean - description: | - Validate the parameters and error if invalid. - - schema_filename: - type: string - description: | - The filename of the schema to validate against. -output: - - dummy_emit: - type: boolean - description: | - Dummy emit to make nf-core subworkflows lint happy -authors: - - "@adamrtalbot" -maintainers: - - "@adamrtalbot" - - "@maxulysse" diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test deleted file mode 100644 index 5784a33f..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ /dev/null @@ -1,200 +0,0 @@ -nextflow_workflow { - - name "Test Workflow UTILS_NFVALIDATION_PLUGIN" - script "../main.nf" - workflow "UTILS_NFVALIDATION_PLUGIN" - tag "subworkflows" - tag "subworkflows_nfcore" - tag "plugin/nf-validation" - tag "'plugin/nf-validation'" - tag "utils_nfvalidation_plugin" - tag "subworkflows/utils_nfvalidation_plugin" - - test("Should run nothing") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success } - ) - } - } - - test("Should run help") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with command") { - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = null - post_help_text = null - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } } - ) - } - } - - test("Should run help with extra text") { - - - when { - - params { - monochrome_logs = true - test_data = '' - } - workflow { - """ - help = true - workflow_command = "nextflow run noorg/doesntexist" - pre_help_text = "pre-help-text" - post_help_text = "post-help-text" - validate_params = false - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.success }, - { assert workflow.exitStatus == 0 }, - { assert workflow.stdout.any { it.contains('pre-help-text') } }, - { assert workflow.stdout.any { it.contains('nextflow run noorg/doesntexist') } }, - { assert workflow.stdout.any { it.contains('Input/output options') } }, - { assert workflow.stdout.any { it.contains('--outdir') } }, - { assert workflow.stdout.any { it.contains('post-help-text') } } - ) - } - } - - test("Should validate params") { - - when { - - params { - monochrome_logs = true - test_data = '' - outdir = 1 - } - workflow { - """ - help = false - workflow_command = null - pre_help_text = null - post_help_text = null - validate_params = true - schema_filename = "$moduleTestDir/nextflow_schema.json" - - input[0] = help - input[1] = workflow_command - input[2] = pre_help_text - input[3] = post_help_text - input[4] = validate_params - input[5] = schema_filename - """ - } - } - - then { - assertAll( - { assert workflow.failed }, - { assert workflow.stdout.any { it.contains('ERROR ~ ERROR: Validation of pipeline parameters failed!') } } - ) - } - } -} diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml deleted file mode 100644 index 60b1cfff..00000000 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfvalidation_plugin: - - subworkflows/nf-core/utils_nfvalidation_plugin/** diff --git a/workflows/airrflow.nf b/workflows/airrflow.nf index 4d228544..93bda121 100644 --- a/workflows/airrflow.nf +++ b/workflows/airrflow.nf @@ -43,6 +43,7 @@ include { CLONAL_ANALYSIS } from '../subworkflows/local/clonal_ana include { REPERTOIRE_ANALYSIS_REPORTING } from '../subworkflows/local/repertoire_analysis_reporting' include { SC_RAW_INPUT } from '../subworkflows/local/sc_raw_input' include { FASTQ_INPUT_CHECK } from '../subworkflows/local/fastq_input_check' +include { RNASEQ_INPUT } from '../subworkflows/local/rnaseq_input' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -54,7 +55,7 @@ include { FASTQ_INPUT_CHECK } from '../subworkflows/local/fastq_inpu // MODULE: Installed directly from nf-core/modules // include { MULTIQC } from '../modules/nf-core/multiqc/main' -include { paramsSummaryMap } from 'plugin/nf-validation' +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_airrflow_pipeline' @@ -68,7 +69,7 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_airr workflow AIRRFLOW { take: - ch_input + ch_input // channel: samplesheet read in from --input main: @@ -94,24 +95,51 @@ workflow AIRRFLOW { ch_validated_samplesheet = SC_RAW_INPUT.out.samplesheet.collect() - ch_presto_filterseq_logs = Channel.empty() - ch_presto_maskprimers_logs = Channel.empty() - ch_presto_pairseq_logs = Channel.empty() - ch_presto_clustersets_logs = Channel.empty() - ch_presto_buildconsensus_logs = Channel.empty() - ch_presto_postconsensus_pairseq_logs = Channel.empty() - ch_presto_assemblepairs_logs = Channel.empty() - ch_presto_collapseseq_logs = Channel.empty() - ch_presto_splitseq_logs = Channel.empty() - ch_fastp_html = Channel.empty() - ch_fastp_json = Channel.empty() - ch_fastqc_postassembly_mqc = Channel.empty() - } else { - // Perform sequence assembly if input type is fastq from bulk sequencing data - SEQUENCE_ASSEMBLY( - ch_input, - DATABASES.out.igblast.collect() - ) + ch_presto_filterseq_logs = Channel.empty() + ch_presto_maskprimers_logs = Channel.empty() + ch_presto_pairseq_logs = Channel.empty() + ch_presto_clustersets_logs = Channel.empty() + ch_presto_buildconsensus_logs = Channel.empty() + ch_presto_postconsensus_pairseq_logs = Channel.empty() + ch_presto_assemblepairs_logs = Channel.empty() + ch_presto_collapseseq_logs = Channel.empty() + ch_presto_splitseq_logs = Channel.empty() + ch_fastp_html = Channel.empty() + ch_fastp_json = Channel.empty() + ch_fastqc_postassembly_mqc = Channel.empty() + + } else if (params.library_generation_method == "trust4") { + // Extract VDJ sequences from "general" RNA seq data using TRUST4 + + RNASEQ_INPUT ( + ch_input, + DATABASES.out.igblast.collect() + ) + + ch_fasta = RNASEQ_INPUT.out.fasta + ch_versions = ch_versions.mix(RNASEQ_INPUT.out.versions) + + ch_validated_samplesheet = RNASEQ_INPUT.out.samplesheet.collect() + + ch_presto_filterseq_logs = Channel.empty() + ch_presto_maskprimers_logs = Channel.empty() + ch_presto_pairseq_logs = Channel.empty() + ch_presto_clustersets_logs = Channel.empty() + ch_presto_buildconsensus_logs = Channel.empty() + ch_presto_postconsensus_pairseq_logs = Channel.empty() + ch_presto_assemblepairs_logs = Channel.empty() + ch_presto_collapseseq_logs = Channel.empty() + ch_presto_splitseq_logs = Channel.empty() + ch_fastp_html = RNASEQ_INPUT.out.fastp_reads_html + ch_fastp_json = RNASEQ_INPUT.out.fastp_reads_json + ch_fastqc_postassembly_mqc = Channel.empty() + } + else { + // Perform sequence assembly if input type is fastq from bulk sequencing data + SEQUENCE_ASSEMBLY( + ch_input, + DATABASES.out.igblast.collect() + ) ch_fasta = SEQUENCE_ASSEMBLY.out.fasta ch_versions = ch_versions.mix(SEQUENCE_ASSEMBLY.out.versions) @@ -246,7 +274,6 @@ workflow AIRRFLOW { ) } ch_versions = ch_versions.mix( REPERTOIRE_ANALYSIS_REPORTING.out.versions ) - ch_versions.dump(tag: "channel_versions") // // Collate and save software versions @@ -254,7 +281,7 @@ workflow AIRRFLOW { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: 'nf_core_pipeline_software_mqc_versions.yml', + name: 'nf_core_' + 'pipeline_software_' + 'mqc_' + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } @@ -281,7 +308,9 @@ workflow AIRRFLOW { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_report_logo.toList() + ch_report_logo.toList(), + [], + [] ) multiqc_report = MULTIQC.out.report.toList() } else {