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Template update for nf-core/tools version 2.13.2.dev0
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-169
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‎.editorconfig

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@@ -28,10 +28,6 @@ indent_style = unset
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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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@@ -8,12 +8,12 @@ on:
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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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@@ -5,13 +5,13 @@ name: nf-core AWS test
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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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@@ -28,10 +28,10 @@ jobs:
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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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‎.github/workflows/download_pipeline.yml

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@@ -14,6 +14,8 @@ on:
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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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@@ -13,7 +13,7 @@ jobs:
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runs-on: ubuntu-latest
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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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run: pip install pre-commit

‎.github/workflows/linting.yml

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pre-commit:
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runs-on: ubuntu-latest
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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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python-version: "3.12"
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cache: "pip"
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- name: Install pre-commit
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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: linting.yml
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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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id: get_topics
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run: |
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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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- uses: rzr/fediverse-action@master
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with:
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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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steps:
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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: "2.13.2.dev0"

‎.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:

‎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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‎assets/nf-core-demo_logo_light.png

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‎conf/base.config

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errorStrategy = 'retry'
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maxRetries = 2
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}
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withName:CUSTOM_DUMPSOFTWAREVERSIONS {
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cache = false
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}
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}

‎conf/modules.config

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ext.args = '--quiet'
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}
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withName: CUSTOM_DUMPSOFTWAREVERSIONS {
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publishDir = [
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path: { "${params.outdir}/pipeline_info" },
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mode: params.publish_dir_mode,
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pattern: '*_versions.yml'
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]
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}
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withName: 'MULTIQC' {
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ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
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publishDir = [

‎conf/test.config

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// Input data
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// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
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input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
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// Genome references
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genome = 'R64-1-1'

‎conf/test_full.config

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// Input data for full size test
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// TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
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// TODO nf-core: Give any required params for the test so that command line flags are not needed
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
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input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
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// Genome references
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genome = 'R64-1-1'

‎docs/images/nf-core-demo_logo_dark.png

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‎docs/images/nf-core-demo_logo_light.png

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‎docs/usage.md

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- A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/)
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- `apptainer`
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- A generic configuration profile to be used with [Apptainer](https://apptainer.org/)
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- `wave`
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- A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
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- `conda`
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- A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
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‎modules.json

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"nf-core": {
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"fastqc": {
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"branch": "master",
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"git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c",
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"git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
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"installed_by": ["modules"]
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},
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"multiqc": {
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},
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"utils_nfcore_pipeline": {
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"branch": "master",
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"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
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"git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
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"installed_by": ["subworkflows"]
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},
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"utils_nfvalidation_plugin": {

‎modules/nf-core/fastqc/main.nf

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