Fix bugs in the GERP step of the pipeline #83
Workflow file for this run
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name: gerp | |
on: | |
push: | |
paths-ignore: | |
- 'README.md' | |
- 'LICENSE.md' | |
- 'workflow/rules/1.2_map_to_mitogenomes.smk' | |
- 'workflow/rules/7_mlRho.smk' | |
- 'workflow/rules/10_pca.smk' | |
- 'workflow/rules/11_ROH.smk' | |
- 'workflow/rules/12_snpEff.smk' | |
branches: | |
- main | |
pull_request: | |
paths-ignore: | |
- 'README.md' | |
- 'LICENSE.md' | |
- 'workflow/docker' | |
- 'workflow/rules/1.2_map_to_mitogenomes.smk' | |
- 'workflow/rules/7_mlRho.smk' | |
- 'workflow/rules/10_pca.smk' | |
- 'workflow/rules/11_ROH.smk' | |
- 'workflow/rules/12_snpEff.smk' | |
branches: | |
- main | |
- dev | |
jobs: | |
test: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: eWaterCycle/setup-apptainer@v2 | |
with: | |
apptainer-version: 1.1.4 | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
miniforge-variant: Mambaforge | |
channels: conda-forge,bioconda | |
activate-environment: generode | |
environment-file: environment.yml | |
auto-activate-base: false | |
- name: conda_environment | |
shell: bash -l {0} | |
run: | | |
conda info | |
conda list | |
- name: Free Up GitHub Actions Ubuntu Runner Disk Space 🔧 | |
uses: jlumbroso/free-disk-space@main | |
with: | |
# This might remove tools that are actually needed, if set to "true" but frees about 6 GB | |
tool-cache: false | |
# All of these default to true, but feel free to set to "false" if necessary for your workflow | |
android: true | |
dotnet: true | |
haskell: true | |
large-packages: true | |
swap-storage: true | |
- name: gerp_dry | |
shell: bash -l {0} | |
run: | | |
snakemake -np -k --configfile .test/config/config_gerp.yaml -j 4 --cores 1 --use-singularity | |
- name: gerp | |
shell: bash -l {0} | |
run: | | |
snakemake -k --configfile .test/config/config_gerp.yaml -j 4 --cores 1 --use-singularity |