mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-25 21:49:55 +00:00
113 lines
3.9 KiB
YAML
113 lines
3.9 KiB
YAML
name: nf-core 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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env:
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NXF_ANSI_LOG: false
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jobs:
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test:
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name: Run pipeline with test data
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# Only run on push if this is the nf-core dev branch (merged PRs)
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if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}"
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runs-on: ubuntu-latest
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strategy:
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matrix:
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NXF_VER:
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- "21.10.3"
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- "latest-everything"
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parameters:
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- "--perform_longread_qc false"
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- "--perform_shortread_qc false"
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- "--shortread_qc_tool fastp"
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- "--shortread_qc_tool fastp --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
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- "--shortread_qc_tool fastp --shortread_qc_mergepairs"
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- "--shortread_qc_tool adapterremoval"
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- "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
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- "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs"
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- "--shortread_complexityfilter_tool bbduk"
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- "--shortread_complexityfilter_tool prinseqplusplus"
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- "--perform_runmerging"
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- "--perform_runmerging --shortread_qc_mergepairs"
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- "--shortread_complexityfilter false --perform_shortread_hostremoval"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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with:
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version: "${{ matrix.NXF_VER }}"
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- name: Show current locale
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run: locale
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- name: Set UTF-8 enabled locale
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run: |
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sudo locale-gen en_US.UTF-8
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sudo update-locale LANG=en_US.UTF-8
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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 ${{ matrix.parameters }}
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motus:
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name: Test mOTUs with workflow parameters
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
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runs-on: ubuntu-latest
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env:
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NXF_VER: ${{ matrix.nxf_ver }}
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NXF_ANSI_LOG: false
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strategy:
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matrix:
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# Nextflow versions
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include:
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# Test pipeline minimum Nextflow version
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- NXF_VER: "21.10.3"
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NXF_EDGE: ""
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# Test latest edge release of Nextflow
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- NXF_VER: ""
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NXF_EDGE: "1"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.NXF_VER }}
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# Uncomment only if the edge release is more recent than the latest stable release
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# See https://github.com/nextflow-io/nextflow/issues/2467
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# NXF_EDGE: ${{ matrix.NXF_EDGE }}
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Show current locale
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run: locale
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- name: Set UTF-8 enabled locale
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run: |
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sudo locale-gen en_US.UTF-8
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sudo update-locale LANG=en_US.UTF-8
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- name: Prepare the database
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run: |
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wget https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py
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python downloadDB.py > download_db_log.txt
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echo 'tool,db_name,db_params,db_path' > 'database_motus.csv'
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echo 'motus,db_mOTU,,db_mOTU' >> 'database_motus.csv'
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- name: Run pipeline with test data
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test_motus,docker --outdir ./results --databases ./database_motus.csv
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