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Update nf-hello-gatk to match format in hello-gatk training
Changes: - Uses samplesheet input (with raw Github URLs) - Uses file() on reference data objects instead of channels - Uses reads_bam as channel name - calling_intervals variable becomes intervals
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name: test-pipeline | ||
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on: [push, pull_request] | ||
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# Cancel if a newer run is started | ||
concurrency: | ||
group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | ||
cancel-in-progress: true | ||
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jobs: | ||
nextflow: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- name: Checkout repository | ||
uses: actions/checkout@v2 | ||
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- name: setup-nextflow | ||
uses: nf-core/setup-nextflow@v1 | ||
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- name: run-nextflow | ||
run: nextflow run . |
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https://github.com/seqeralabs/nf-hello-gatk/raw/refs/heads/main/data/bam/reads_mother.bam | ||
https://github.com/seqeralabs/nf-hello-gatk/raw/refs/heads/main/data/bam/reads_father.bam | ||
https://github.com/seqeralabs/nf-hello-gatk/raw/refs/heads/main/data/bam/reads_son.bam |
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