Fix branch name to activate test workflow #1
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| # Upon each push, if anything under episodes/files/ is changed, we would like to: | |
| # | |
| # 1) Download the sample data | |
| # 2) Install the conda environment (episodes/files/conda_env.yaml) | |
| # 3) Test every ep??.Snakefile | |
| # 4) Test the assembly script and the sample answer | |
| # | |
| name: Code sample tests on Ubuntu | |
| on: | |
| push: | |
| branches: [ main ] | |
| paths: ['episodes/files/**', '.test/**', '.github/workflows/code-test-ubuntu.yml'] | |
| jobs: | |
| auto_test: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -eo pipefail -l {0} # Needed for conda | |
| steps: | |
| - uses: actions/checkout@main | |
| # Do this first. It looks like figshare denies downloads after a few times, so we may need | |
| # to mirror the file somewhere else. At least this will fail fast. | |
| # - name: Download the sample data | |
| # run: | | |
| # wget --progress=dot:mega --content-disposition https://figshare.com/ndownloader/files/42467370 | |
| # md5sum -c <<<"4522e76f9dddda13e55f7d283638e628 data-for-snakemake-novice-bioinformatics.tar.xz" | |
| # Let's use this copy for testing. Yes it's in .xz.gz format, otherwise GitHub won't accept it. | |
| - name: Download the sample data from GitHub | |
| run: | | |
| wget --progress=dot:mega \ | |
| https://github.com/user-attachments/files/16439467/data-for-snakemake-novice-bioinformatics.tar.xz.gz | |
| gunzip data-for-snakemake-novice-bioinformatics.tar.xz | |
| md5sum -c <<<"4522e76f9dddda13e55f7d283638e628 data-for-snakemake-novice-bioinformatics.tar.xz" | |
| - name: Install Conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| use-mamba: false | |
| activate-environment: snakemake_carpentry | |
| environment-file: episodes/files/conda_env.yaml | |
| # This only matters for the assembly test, where Snakemake installs packages | |
| - name: Configure Conda as per lesson setup | |
| run: | | |
| cat >~/.condarc <<END | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| solver: libmamba | |
| channel_priority: strict | |
| END | |
| - name: Confirm Snakemake Version | |
| run: | | |
| conda env list | |
| echo --- | |
| which snakemake | |
| snakemake --version | |
| which rename | |
| ( rename --man | head -n 8 ) || true | |
| # Check all the interim answers with fresh data dir | |
| - name: Test interim answers | |
| run: | | |
| for tf in .test/ep*.test.sh ; do | |
| rm -rf snakemake_data | |
| tar -xaf data-for-snakemake-novice-bioinformatics.tar.xz | |
| echo "Running $tf..." | |
| ( set -euo pipefail ; source $tf ) | |
| printf '\n-\n' | |
| done | |
| # Test the shadow demo | |
| - name: Test shadow demo | |
| run: | | |
| for tf in .test/shadow.test.sh ; do | |
| rm -rf snakemake_data | |
| mkdir snakemake_data | |
| echo "Running $tf..." | |
| ( set -euo pipefail ; source $tf ) | |
| printf '\n-\n' | |
| done | |
| # Check the sample script and the solution to the larger exercise | |
| - name: Test assembly BASH script and Snakefile | |
| run: | | |
| for tf in .test/assembly_*.test.sh ; do | |
| rm -rf snakemake_data | |
| tar -xaf data-for-snakemake-novice-bioinformatics.tar.xz | |
| echo "Running $tf..." | |
| ( set -euo pipefail ; source $tf ) | |
| printf '\n-\n' | |
| done |