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Merge pull request #1460 from nf-core/dev
Release 3.4.1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| name: test | ||
| name: nf-core CI | ||
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | ||
| on: | ||
| pull_request: | ||
|
|
@@ -28,7 +28,7 @@ jobs: | |
| # Expose matched filters as job 'tags' output variable | ||
| tags: ${{ steps.filter.outputs.changes }} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: actions/checkout@v4 | ||
|
|
||
| - uses: frouioui/paths-filter@main | ||
| id: filter | ||
|
|
@@ -52,14 +52,25 @@ jobs: | |
| NXF_VER: | ||
| - "23.04.0" | ||
| - "latest-everything" | ||
| exclude: | ||
| - tags: "sentieon/bwamem" | ||
| - tags: "sentieon/dedup" | ||
| - tags: "sentieon/dnascope" | ||
| - tags: "sentieon/dnascope_joint_germline" | ||
| - tags: "sentieon/dnascope_skip_filter" | ||
| - tags: "sentieon/haplotyper" | ||
| - tags: "sentieon/haplotyper_joint_germline" | ||
| - tags: "sentieon/haplotyper_skip_filter" | ||
| - NXF_VER: "latest-everything" | ||
| tags: "joint_germline" | ||
| env: | ||
| NXF_ANSI_LOG: false | ||
| TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | ||
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | ||
|
|
||
| steps: | ||
| - name: Check out pipeline code | ||
| uses: actions/checkout@v3 | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Hash Github Workspace | ||
| id: hash_workspace | ||
|
|
@@ -105,7 +116,7 @@ jobs: | |
|
|
||
| - name: Check out test data | ||
| if: steps.cache-testdata.outputs.cache-hit != 'true' | ||
| uses: actions/checkout@v3 | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| repository: nf-core/test-datasets | ||
| ref: sarek3 | ||
|
|
@@ -136,6 +147,9 @@ jobs: | |
| if: matrix.profile == 'conda' | ||
| run: conda clean -a | ||
|
|
||
| - name: Disk space cleanup | ||
| uses: jlumbroso/[email protected] | ||
|
|
||
| - name: Run pytest-workflow | ||
| uses: Wandalen/wretry.action@v1 | ||
| with: | ||
|
|
@@ -168,7 +182,7 @@ jobs: | |
| tags: ${{ steps.filter.outputs.changes }} | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: actions/checkout@v4 | ||
|
|
||
| - name: Combine all tags.yml files | ||
| id: get_tags | ||
|
|
@@ -200,29 +214,65 @@ jobs: | |
| - "23.04.0" | ||
| - "latest-everything" | ||
| exclude: | ||
| - tags: "bcftools/concat" | ||
| - tags: "bcftools/mpileup" | ||
| - tags: "bcftools/sort" | ||
| - tags: "bwa/index" | ||
| - tags: "bwa/mem" | ||
| - tags: "bwamem2/index" | ||
| - tags: "bwamem2/mem" | ||
| - tags: "cat/cat" | ||
| - tags: "cat/fastq" | ||
| - tags: "custom/dumpsoftwareversions" | ||
| - tags: "cnvkit/batch" | ||
| - tags: "deepvariant" | ||
| - tags: "dragmap/align" | ||
| - tags: "dragmap/hashtable" | ||
| - tags: "ensemblvep/download" | ||
| - tags: "ensemblvep/vep" | ||
| - tags: "fastp" | ||
| - tags: "fastqc" | ||
| - tags: "fgbio/fastqtobam" | ||
| - tags: "freebayes" | ||
| - tags: "gatk4/applybqsr" | ||
| - tags: "gatk4/baserecalibrator" | ||
| - tags: "gatk4/estimatelibrarycomplexity" | ||
| - tags: "gatk4/genomicsdbimport" | ||
| - tags: "gatk4/haplotypecaller" | ||
| - tags: "gatk4/markduplicates" | ||
| - tags: "gatk4/mergevcfs" | ||
| - tags: "gatk4/mutect2" | ||
| - tags: "gatk4spark/applybqsr" | ||
| - tags: "gatk4spark/markduplicates" | ||
| - tags: "mosdepth" | ||
| - tags: "multiqc" | ||
| - tags: "samblaster" | ||
| - tags: "samtools/mpileup" | ||
| - tags: "samtools/stats" | ||
| - tags: "snpeff/snpeff" | ||
| - tags: "strelka/germline" | ||
| - tags: "strelka/somatic" | ||
| - tags: "subworkflows/utils_nfvalidation_plugin" | ||
| - tags: "tabix/bgziptabix" | ||
| - tags: "tabix/tabix" | ||
| - tags: "tiddit/sv" | ||
| - tags: "untar" | ||
| env: | ||
| NXF_ANSI_LOG: false | ||
| TEST_DATA_BASE: "${{ github.workspace }}/test-datasets" | ||
| SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }} | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - uses: actions/checkout@v4 | ||
|
|
||
| - uses: actions/setup-java@v3 | ||
| with: | ||
| distribution: "temurin" | ||
| java-version: "17" | ||
| - name: Setup Nextflow | ||
|
|
||
| - name: Install Nextflow ${{ matrix.NXF_VER }} | ||
| uses: nf-core/setup-nextflow@v1 | ||
| with: | ||
| version: "${{ matrix.NXF_VER }}" | ||
|
|
||
| - name: Cache nf-test installation | ||
| id: cache-software | ||
|
|
@@ -277,6 +327,9 @@ jobs: | |
| SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0) | ||
| nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64 | ||
| - name: Disk space cleanup | ||
| uses: jlumbroso/[email protected] | ||
|
|
||
| # Test the module | ||
| - name: Run nf-test | ||
| run: | | ||
|
|
||
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