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Merge branch 'rel-0.5.0'
2 parents 2d5713f + b22373f commit 1ebec86

29 files changed

Lines changed: 1536 additions & 822 deletions

‎.github/dependabot.yml‎

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directory: "/"
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schedule:
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interval: "daily"
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target-branch: "dev"

‎.github/workflows/docker-image.yml‎

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username: ${{ secrets.DOCKER_HUB_USERNAME }}
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password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
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- name: Set platforms
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id: set_platforms
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run: |
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echo "github ref: ${GITHUB_REF}"
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if [[ "${GITHUB_REF##*/}" == "main" || "${GITHUB_REF##*/}" == "dev" ]]; then
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echo "platforms=linux/amd64,linux/arm64" >> $GITHUB_OUTPUT
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else
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echo "platforms=linux/amd64" >> $GITHUB_OUTPUT
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fi
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- name: Build and push
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uses: docker/build-push-action@v6
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with:
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context: .
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platforms: linux/amd64,linux/arm64
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platforms: ${{ steps.set_platforms.outputs.platforms }}
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push: true
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#${{ github.event_name != 'push' && github.event_name != 'pull_request' }}
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tags: ${{ steps.meta.outputs.tags }}

‎.github/workflows/nf-test.yml‎

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name: nf-test CI
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# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
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on:
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push:
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branches:
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- dev
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pull_request:
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release:
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types: [published]
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workflow_dispatch:
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env:
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NFT_DIFF: "pdiff"
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NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
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NFT_VER: "0.9.2"
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NFT_WORKDIR: "${{ github.workspace }}/nf-test-work"
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NXF_ANSI_LOG: false
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NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
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NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
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concurrency:
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group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
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cancel-in-progress: true
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jobs:
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test:
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runs-on: ubuntu-latest
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name: "Test ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/5"
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strategy:
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fail-fast: false
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matrix:
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NXF_VER:
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- "24.10.2"
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- "latest-everything"
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filter: ["pipeline"]
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# filter: ["process", "workflow", "function", "pipeline"]
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profile: ["conda", "docker", "singularity"]
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shard: [1]
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# shard: [1, 2, 3, 4, 5]
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
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with:
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fetch-depth: 0
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- uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
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with:
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python-version: "3.11"
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- uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
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with:
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distribution: "temurin"
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java-version: "17"
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- name: Set up Nextflow
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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: Set up nf-test
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uses: nf-core/setup-nf-test@v1
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with:
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version: ${{ env.NFT_VER }}
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- name: Set up apptainer
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if: matrix.profile == 'singularity'
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uses: eWaterCycle/setup-apptainer@main
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- name: Set up Singularity
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if: matrix.profile == 'singularity'
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run: |
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mkdir -p $NXF_SINGULARITY_CACHEDIR
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mkdir -p $NXF_SINGULARITY_LIBRARYDIR
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- name: Install pdiff
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run: python -m pip install --upgrade pip pdiff cryptography
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- name: Set up miniconda
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if: matrix.profile == 'conda'
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uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
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with:
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miniconda-version: "latest"
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auto-update-conda: true
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conda-solver: libmamba
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channels: conda-forge,bioconda
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- name: Set up Conda
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if: matrix.profile == 'conda'
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run: |
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echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
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echo $(realpath python) >> $GITHUB_PATH
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#- name: Disk space cleanup
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# uses: jlumbroso/free-disk-space@v1.3.1
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- name: Start summary
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id: print-test
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run: |
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echo "## nf-test tests summary :rocket:" >> $GITHUB_STEP_SUMMARY
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echo "" >> $GITHUB_STEP_SUMMARY
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echo "This \`${{ matrix.filter }}\` ${{ matrix.shard }}/5 shard was run on \`${{ matrix.profile }}\` | \`NXF_VER=${{ matrix.NXF_VER }}\`, and contains the following test(s):" >> $GITHUB_STEP_SUMMARY
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echo "" >> $GITHUB_STEP_SUMMARY
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nf-test test \
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--ci \
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--dryRun \
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--junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
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--shard ${{ matrix.shard }}/1 \
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--follow-dependencies \
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--profile "+${{ matrix.profile }}" \
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--filter ${{ matrix.filter }} \
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| grep PASSED | cut -d "'" -f 2 | sed 's/^/- /' | sort -u >> $GITHUB_STEP_SUMMARY
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- name: "Run tests | ${{ matrix.filter }}_${{ matrix.profile }} | ${{ matrix.shard }}/1"
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run: |
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nf-test test \
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--ci \
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--debug \
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--verbose \
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--junitxml="TEST-${{ matrix.filter }}_${{ matrix.profile }}_${{ matrix.shard }}.xml" \
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--shard ${{ matrix.shard }}/1 \
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--follow-dependencies \
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--profile "+${{ matrix.profile }}" \
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--filter ${{ matrix.filter }}
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- name: Print success in summary
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if: success()
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run: |
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echo "" >> $GITHUB_STEP_SUMMARY
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echo "All test(s) successfull :tada:" >> $GITHUB_STEP_SUMMARY
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- name: Print failure in summary
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if: failure()
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run: |
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echo "" >> $GITHUB_STEP_SUMMARY
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echo "Some test(s) failed :cold_sweat:" >> $GITHUB_STEP_SUMMARY
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- name: Publish Test Report
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uses: mikepenz/action-junit-report@v4
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if: success() || failure() # always run even if the previous step fails
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with:
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report_paths: "TEST-*.xml"
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- name: Upload test results
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if: always() # run even if tests fail
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uses: actions/upload-artifact@v4
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with:
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name: nf-test-results-${{ matrix.filter }}-${{ matrix.profile }}-${{ matrix.NXF_VER }}-${{ matrix.shard }}
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path: |
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TEST-*.xml
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${{ env.NFT_WORKDIR }}/**/output/**
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retention-days: 4
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- name: Clean up
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if: success() || failure()
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run: |
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sudo rm -rf /home/ubuntu/tests/

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