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Try separating MALT
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2 changed files with 34 additions and 1 deletions
33
.github/workflows/ci.yml
vendored
33
.github/workflows/ci.yml
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@ -134,3 +134,36 @@ jobs:
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with:
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command: nextflow run ${GITHUB_WORKSPACE} -profile test_krakenuniq,docker --outdir ./results
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attempt_limit: 3
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malt:
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name: Test MALT with workflow parameters
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if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/taxprofiler') }}
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runs-on: ubuntu-latest
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strategy:
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matrix:
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NXF_VER:
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- "21.10.3"
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- "latest-everything"
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steps:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Install Nextflow
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uses: nf-core/setup-nextflow@v1
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with:
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version: "${{ 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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uses: Wandalen/wretry.action@v1.0.11
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with:
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command: nextflow run ${GITHUB_WORKSPACE} -profile test_nothing,docker --run_malt --outdir ./results
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attempt_limit: 3
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@ -35,7 +35,7 @@ params {
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run_kaiju = true
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run_kraken2 = true
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run_bracken = true
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run_malt = true
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run_malt = false
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run_metaphlan3 = true
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run_centrifuge = true
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run_diamond = true
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