fix: issue when input files are in subfolders #5833
Workflow file for this run
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| name: Code quality | |
| on: | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| formatting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: fmt | |
| channels: "conda-forge, bioconda" | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| - name: Setup environment | |
| shell: bash -el {0} | |
| run: | | |
| conda config --set channel_priority strict | |
| mamba install -n fmt -y black snakefmt | |
| - name: Check Python formatting | |
| shell: bash -el {0} | |
| run: | | |
| black --check */*/*/wrapper.py */*/wrapper.py | |
| # TODO reactivate once comment errors are fixed | |
| # - name: Check Snakemake formatting | |
| # run: | | |
| # export PATH="/usr/share/miniconda/bin:$PATH" | |
| # source activate fmt | |
| # snakefmt --check $(git diff origin/master --name-only | grep Snakefile) | |
| linting: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v1 | |
| - name: Setup mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: snakemake | |
| channels: "conda-forge, bioconda" | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| - name: Setup Snakemake environment | |
| shell: bash -el {0} | |
| run: | | |
| conda config --set channel_priority strict | |
| mamba install -n snakemake -y snakemake-minimal snakemake | |
| - name: Fetch master | |
| run: | | |
| git fetch origin master | |
| - name: Linting | |
| shell: bash -el {0} | |
| run: | | |
| declare -i ERRORS=0 | |
| # get all modified and added files, not those that are deleted | |
| for f in $(git diff origin/master --name-only --diff-filter=d | grep Snakefile) | |
| do | |
| snakemake -s $f --lint | |
| ERRORS+=$? | |
| done | |
| if (( $ERRORS > 0 )) | |
| then | |
| echo "There are some lints above. Please fix them." | |
| exit 1 | |
| fi |