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feat: Replace mutect2_par with snakemake scattergather #179

feat: Replace mutect2_par with snakemake scattergather

feat: Replace mutect2_par with snakemake scattergather #179

Workflow file for this run

name: Tests
on:
# always run tests when pushing to main
push:
branches: [ main ]
# only run tests on pull requests which actually modify files that affect the tests
pull_request:
branches_ignore: []
# for now, the tests defined in this file are only run when any of the following paths are modified:
paths:
# workflow definitions
- '.tests/**'
# github workflow configurations
- '.github/**'
# 'base' files of snappy-pipeline
- 'snappy_pipeline/*'
- 'snappy_pipeline/workflows/abstract/**'
# steps used in the test workflows
- 'snappy_pipeline/workflows/ngs_mapping/**'
- 'snappy_pipeline/workflows/somatic_variant_calling/**'
- 'snappy_pipeline/workflows/somatic_variant_annotation/**'
- 'snappy_pipeline/workflows/somatic_variant_filtration/**'
# 'base' files of snappy_wrappers
- 'snappy_wrappers/*'
# wrappers used in the test workflows
- 'snappy_wrappers/wrappers/alfred/**'
- 'snappy_wrappers/wrappers/bcftools/**'
- 'snappy_wrappers/wrappers/bwa/**'
- 'snappy_wrappers/wrappers/link_in_bam/**'
- 'snappy_wrappers/wrappers/mutect/**'
- 'snappy_wrappers/wrappers/mutect_par/**'
- 'snappy_wrappers/wrappers/mutect2/**'
- 'snappy_wrappers/wrappers/mutect2_par/**'
- 'snappy_wrappers/wrappers/ngs_chew/**'
- 'snappy_wrappers/wrappers/somatic_variant_filtration/**'
- 'snappy_wrappers/wrappers/vep/**'
jobs:
Dryrun_Tests:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
with:
lfs: 'true'
- name: Test workflow (local FASTQs)
uses: snakemake/snakemake-github-action@v1
with:
directory: .tests/test-workflow
snakefile: .tests/test-workflow/workflow/Snakefile
args: "--configfile .tests/test-workflow/config/config.yaml --use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache --dryrun"
show-disk-usage-on-error: true
Tests:
runs-on: ubuntu-latest
needs:
- Dryrun_Tests
steps:
- name: update apt
run: sudo apt-get update
- uses: actions/checkout@v4
with:
lfs: 'true'
- name: Test workflow (local FASTQs)
uses: snakemake/snakemake-github-action@v1
with:
directory: .tests/test-workflow
snakefile: .tests/test-workflow/workflow/Snakefile
args: "--configfile .tests/test-workflow/config/config.yaml --use-conda --show-failed-logs -j 2 --conda-cleanup-pkgs cache"
show-disk-usage-on-error: true