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Merge pull request #5 from nf-core/dev
Release of nf-core/demo
2 parents a645f20 + 2ce1fb7 commit 705f18e

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‎.editorconfig

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[/assets/email*]
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indent_size = unset
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# ignore Readme
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[README.md]
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indent_style = unset
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# ignore python
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# ignore python and markdown
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[*.{py,md}]
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indent_style = unset

‎.github/PULL_REQUEST_TEMPLATE.md

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@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/demo
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- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/demo/tree/master/.github/CONTRIBUTING.md)
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- [ ] If necessary, also make a PR on the nf-core/demo _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
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- [ ] Make sure your code lints (`nf-core lint`).
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- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
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- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
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- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
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- [ ] Usage Documentation in `docs/usage.md` is updated.
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- [ ] Output Documentation in `docs/output.md` is updated.

‎.github/workflows/awsfulltest.yml

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types: [published]
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workflow_dispatch:
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jobs:
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run-tower:
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run-platform:
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name: Run AWS full tests
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if: github.repository == 'nf-core/demo'
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runs-on: ubuntu-latest
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steps:
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- name: Launch workflow via tower
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- name: Launch workflow via Seqera Platform
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uses: seqeralabs/action-tower-launch@v2
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# TODO nf-core: You can customise AWS full pipeline tests as required
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# Add full size test data (but still relatively small datasets for few samples)
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- uses: actions/upload-artifact@v4
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with:
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name: Tower debug log file
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name: Seqera Platform debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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seqera_platform_action_*.log
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seqera_platform_action_*.json

‎.github/workflows/awstest.yml

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on:
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workflow_dispatch:
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jobs:
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run-tower:
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run-platform:
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name: Run AWS tests
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if: github.repository == 'nf-core/demo'
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runs-on: ubuntu-latest
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steps:
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# Launch workflow using Tower CLI tool action
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- name: Launch workflow via tower
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# Launch workflow using Seqera Platform CLI tool action
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- name: Launch workflow via Seqera Platform
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uses: seqeralabs/action-tower-launch@v2
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with:
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workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
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- uses: actions/upload-artifact@v4
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with:
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name: Tower debug log file
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name: Seqera Platform debug log file
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path: |
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tower_action_*.log
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tower_action_*.json
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seqera_platform_action_*.log
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seqera_platform_action_*.json

‎.github/workflows/ci.yml

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- "latest-everything"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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uses: nf-core/setup-nextflow@v2
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with:
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version: "${{ matrix.NXF_VER }}"
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- name: Disk space cleanup
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uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
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- name: Run pipeline with test data
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# TODO nf-core: You can customise CI pipeline run tests as required
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# For example: adding multiple test runs with different parameters
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# Remember that you can parallelise this by using strategy.matrix
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

‎.github/workflows/download_pipeline.yml

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pull_request:
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types:
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- opened
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- edited
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- synchronize
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branches:
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- master
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pull_request_target:
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runs-on: ubuntu-latest
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steps:
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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uses: nf-core/setup-nextflow@v2
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- name: Disk space cleanup
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uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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with:
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python-version: "3.11"
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python-version: "3.12"
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architecture: "x64"
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- uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
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with:
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- name: Inspect download
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run: tree ./${{ env.REPOTITLE_LOWERCASE }}
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- name: Run the downloaded pipeline
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- name: Run the downloaded pipeline (stub)
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id: stub_run_pipeline
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continue-on-error: true
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env:
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NXF_SINGULARITY_CACHEDIR: ./
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NXF_SINGULARITY_HOME_MOUNT: true
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run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
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- name: Run the downloaded pipeline (stub run not supported)
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id: run_pipeline
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if: ${{ job.steps.stub_run_pipeline.status == failure() }}
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env:
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NXF_SINGULARITY_CACHEDIR: ./
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NXF_SINGULARITY_HOME_MOUNT: true
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run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results

‎.github/workflows/fix-linting.yml

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steps:
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# Use the @nf-core-bot token to check out so we can push later
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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with:
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token: ${{ secrets.nf_core_bot_auth_token }}
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GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
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# Install and run pre-commit
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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with:
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python-version: 3.11
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python-version: "3.12"
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- name: Install pre-commit
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‎.github/workflows/linting.yml

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pre-commit:
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steps:
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- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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- uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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- name: Set up Python 3.11
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uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- name: Set up Python 3.12
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uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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with:
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python-version: 3.11
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cache: "pip"
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python-version: "3.12"
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runs-on: ubuntu-latest
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
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uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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uses: nf-core/setup-nextflow@v2
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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with:
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python-version: "3.11"
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python-version: "3.12"
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architecture: "x64"
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- name: Install dependencies
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- name: Upload linting log file artifact
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if: ${{ always() }}
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uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
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uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
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with:
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name: linting-logs
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path: |

‎.github/workflows/linting_comment.yml

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runs-on: ubuntu-latest
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steps:
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- name: Download lint results
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uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
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uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
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with:
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workflow_conclusion: completed

‎.github/workflows/release-announcements.yml

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- name: get topics and convert to hashtags
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curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
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echo "topics=$(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
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Please see the changelog: ${{ github.event.release.html_url }}
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${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
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${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
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send-tweet:
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runs-on: ubuntu-latest
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- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
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- uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
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with:
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python-version: "3.10"
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- name: Install dependencies

‎.nf-core.yml

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repository_type: pipeline
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nf_core_version: "2.14.1"

‎.pre-commit-config.yaml

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rev: "v3.1.0"
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hooks:
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- id: prettier
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additional_dependencies:
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- prettier@3.2.5
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- repo: https://github.com/editorconfig-checker/editorconfig-checker.python
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rev: "2.7.3"
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hooks:

‎CHANGELOG.md

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## v1.0dev - [date]
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## 1.0.0 2024-06-19
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Initial release of nf-core/demo, created with the [nf-core](https://nf-co.re/) template.
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### Credits
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Special thanks to the following for their reviews and assistance:
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- [Maxime Garcia](https://github.com/maxulysse)
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- [Friederike Hanssen](https://github.com/FriederikeHanssen)
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### `Added`
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### `Fixed`
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- `nf-core/seqtk/trim` module
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- `skip_trim` parameter
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### `Dependencies`
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## v1.0dev - 2024-05-5
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### `Deprecated`
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Initial release of nf-core/demo, created with the [nf-core](https://nf-co.re/) template.

‎CITATIONS.md

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> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
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- [seqtk](https://github.com/lh3/seqtk)
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- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
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> 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.

‎README.md

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[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
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[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
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[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
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[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/demo)
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[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/demo)
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[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23demo-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/demo)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
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## Introduction
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**nf-core/demo** is a bioinformatics pipeline that ...
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**nf-core/demo** is a simple nf-core style bioinformatics pipeline for workshops and demonstrations. It was created using the nf-core template and is designed to run quickly using small test data files.
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24-
<!-- TODO nf-core:
25-
Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
26-
major pipeline sections and the types of output it produces. You're giving an overview to someone new
27-
to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
28-
-->
24+
![nf-core/demo metro map](docs/images/nf-core-demo-subway.png)
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30-
<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
31-
workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples. -->
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<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
33-
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1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
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2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
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1. Read QC ([`FASTQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
27+
2. Adapter and quality trimming ([`SEQTK_TRIM`](https://github.com/lh3/seqtk))
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3. Present QC for raw reads ([`MULTIQC`](http://multiqc.info/))
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## Usage
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> [!NOTE]
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> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
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<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
43-
Explain what rows and columns represent. For instance (please edit as appropriate):
44-
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First, prepare a samplesheet with your input data that looks as follows:
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`samplesheet.csv`:
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```csv
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sample,fastq_1,fastq_2
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CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
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SAMPLE1_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz
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SAMPLE2_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz
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SAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,
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SAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,
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```
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Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
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-->
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Now, you can run the pipeline using:
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<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
61-
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```bash
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nextflow run nf-core/demo \
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-profile <docker/singularity/.../institute> \
@@ -80,11 +69,9 @@ For more details about the output files and reports, please refer to the
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## Credits
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nf-core/demo was originally written by Christopher Hakkaart.
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We thank the following people for their extensive assistance in the development of this pipeline:
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nf-core/demo was originally written by Chris Hakkaart ([@christopher-hakkaart](https://github.com/christopher-hakkaart)).
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<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
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<!-- We thank the following people for their extensive assistance in the development of this pipeline: -->
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## Contributions and Support
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@@ -97,8 +84,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
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<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
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<!-- If you use nf-core/demo for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
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<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
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An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
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You can cite the `nf-core` publication as follows:

‎assets/methods_description_template.yml

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section_name: "nf-core/demo Methods Description"
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section_href: "https://github.com/nf-core/demo"
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plot_type: "html"
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## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
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## You inject any metadata in the Nextflow '${workflow}' object
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data: |
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<h4>Methods</h4>

‎assets/multiqc_config.yml

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report_comment: >
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This report has been generated by the <a href="https://github.com/nf-core/demo/tree/dev" target="_blank">nf-core/demo</a>
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This report has been generated by the <a href="https://github.com/nf-core/demo/releases/tag/1.0.0" target="_blank">nf-core/demo</a>
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analysis pipeline. For information about how to interpret these results, please see the
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<a href="https://nf-co.re/demo/dev/docs/output" target="_blank">documentation</a>.
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<a href="https://nf-co.re/demo/1.0.0/docs/output" target="_blank">documentation</a>.
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report_section_order:
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"nf-core-demo-methods-description":
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order: -1000

‎assets/nf-core-demo_logo_light.png

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