add a task for fastq-filter #112
Workflow file for this run
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| name: Linting | |
| on: | |
| pull_request: | |
| paths_ignore: | |
| - "docs/**" | |
| defaults: | |
| run: | |
| # This is needed for miniconda, see: | |
| # https://github.com/marketplace/actions/setup-miniconda#important | |
| shell: bash -l {0} | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| name: Linting checks | |
| steps: | |
| - uses: actions/[email protected] | |
| with: | |
| submodules: recursive | |
| - name: Set cache date | |
| run: echo "DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV | |
| - name: Cache conda environment | |
| # Use an always upload cache to prevent solving conda environment again and again on failing linting. | |
| uses: pat-s/[email protected] | |
| env: | |
| # Increase this value to manually invalidate the cache | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: /usr/share/miniconda/envs/biowdl-lint | |
| key: | |
| ${{runner.os}}-biowdl-lint-${{ env.CACHE_NUMBER }}-${{env.DATE}}-${{ hashFiles('.github/lint-environment.yml') }} | |
| id: env_cache | |
| # Use the builtin conda. This is the fastest installation. It may not be | |
| # the fastest for resolving, but the package cache mitigates that problem. | |
| # Since this installs fastest, it is fastest for all runs where a cache | |
| # hit occurs. | |
| - name: install miniconda | |
| uses: conda-incubator/[email protected] | |
| with: | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: strict | |
| auto-activate-base: false | |
| use-only-tar-bz2: true # Needed for proper caching according to the documentation. | |
| # activate-environment is broken! This always seems to create a new environment. | |
| # Activation is therefore done separately. | |
| - name: Create test environment if no cache is present | |
| run: conda env create -n biowdl-lint -f .github/lint-environment.yml | |
| if: steps.env_cache.outputs.cache-hit != 'true' | |
| - name: Activate test environment | |
| # The new PATH should be passed to the environment, otherwise it won't register. | |
| run: | | |
| conda activate biowdl-lint | |
| echo "PATH=$PATH" >> $GITHUB_ENV | |
| - name: Fetch develop branch for comparisons | |
| run: git fetch --depth=1 origin develop | |
| - name: run womtool validate | |
| # Only check files that have changed from the base reference. | |
| # Womtool validate checks very slowly, so this saves a lot of time. | |
| run: | | |
| set -x | |
| for WDL_FILE in $(git diff --name-only origin/${{github.base_ref}} | grep -E '*.wdl$'); do | |
| womtool validate $WDL_FILE | |
| done | |
| - name: run miniwdl check | |
| run: | | |
| set -x | |
| bash -c 'miniwdl check $(git ls-files *.wdl)' | |
| - name: Check copyright headers | |
| run: | | |
| set -x | |
| for WDL_FILE in $(git diff --name-only origin/${{github.base_ref}} | grep -E '*.wdl$'); do | |
| grep Copyright $WDL_FILE || bash -c "echo No copyright header in $WDL_FILE && exit 1" | |
| done | |
| - name: Check parameter_meta for inputs | |
| run: | | |
| set -x | |
| for WDL_FILE in $(git diff --name-only origin/${{github.base_ref}} | grep -E '*.wdl$'); do | |
| wdl-aid --strict $WDL_FILE > /dev/null 2> wdl-aid_stderr || | |
| if grep -z 'ValueError: Missing parameter_meta for inputs:' wdl-aid_stderr | |
| then | |
| exit 1 | |
| fi | |
| done |