Skip to content

Fix GitHub action dependency error #103

Fix GitHub action dependency error

Fix GitHub action dependency error #103

Workflow file for this run

name: Test
on:
workflow_dispatch:
push:
branches:
- main
- dev
pull_request:
branches:
- "**"
jobs:
skip_duplicate:
permissions:
actions: write
contents: read
runs-on: ubuntu-latest
outputs:
should_skip: ${{ steps.skip_check.outputs.should_skip }}
steps:
- id: skip_check
uses: fkirc/[email protected]
with:
cancel_others: 'true'
concurrent_skipping: 'same_content_newer'
paths_ignore: '["**/README.md", "CITATION.cff"]'
run_test_pipeline:
needs: skip_duplicate
if: ${{ needs.skip_duplicate.outputs.should_skip != 'true' }}
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v3
- name: Setup mamba
uses: conda-incubator/setup-miniconda@v3
with:
mamba-version: "*"
channels: conda-forge,bioconda,defaults
auto-activate-base: true
activate-environment: ""
- name: Install Snakemake 7.32
run: |
pip install snakemake==7.32.4
- name: Run test pipeline
run: |
snakemake --snakefile workflow/Snakefile --directory .test --configfile config/config.yaml .test/targets.yaml --use-conda -c1
- name: Pack logs
shell: bash
run: |
tar czf logs.tar.gz .test/output/logs
- name: Upload output file
uses: actions/upload-artifact@v3
with:
name: output-logs
path: logs.tar.gz