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Fix bugs in the GERP step of the pipeline #83

Fix bugs in the GERP step of the pipeline

Fix bugs in the GERP step of the pipeline #83

Workflow file for this run

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