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Split github actions to reduce run time and disk space #1

Split github actions to reduce run time and disk space

Split github actions to reduce run time and disk space #1

Workflow file for this run

name: snpeff
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/13_GERP.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/13_GERP.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: snpeff_dry
shell: bash -l {0}
run: |
snakemake -npr --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity
- name: snpeff
shell: bash -l {0}
run: |
snakemake --configfile .test/config/config_snpeff.yaml -j 4 --cores 1 --use-singularity