Cleanup Code and Improvements for Release 2.0.0 #64
Workflow file for this run
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| ##################################### | |
| # Nextflow CI Test for NML Pipeline # | |
| ##################################### | |
| name: ncov2019-artic-nf NML CI | |
| on: | |
| pull_request: # Run on all pull requests | |
| push: | |
| branches: master | |
| schedule: # Run master on 5th of each month | |
| - cron: 0 6 5 * * | |
| branches: master | |
| jobs: | |
| pipeline-test: | |
| name: ncov2019-artic-nf nanopore CI tests | |
| runs-on: ubuntu-latest | |
| # For conda | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| # Setup repo | |
| - uses: actions/checkout@v3 | |
| - name: Create artifacts dir | |
| run: mkdir -p artifacts | |
| # Add conda, mamba, and nextflow | |
| - name: Setup Miniconda | |
| uses: conda-incubator/setup-miniconda@v2.2.0 | |
| with: | |
| miniconda-version: "latest" | |
| activate-environment: nextflow | |
| python-version: 3.8 | |
| mamba-version: "*" | |
| use-mamba: true | |
| channels: conda-forge,bioconda,defaults | |
| - name: Install Nextflow | |
| run: | | |
| mamba install nextflow | |
| - name: Nextflow Version | |
| run: | | |
| nextflow -v | |
| conda --version | |
| # Check how repo looks incase there is an issue | |
| - name: List Files | |
| run: | | |
| ls -al ${{ github.workspace }} | |
| # Run Help Command | |
| - name: Pipeline Help CMD | |
| run: | | |
| nextflow run ./main.nf --help | |
| # Unzip fast5s to run | |
| - name: Unzip fast5 files | |
| run: | | |
| cd .github/data/nanopore/fast5_pass/ | |
| gunzip barcode*/*.fast5.gz | |
| cd - | |
| # Run Pipelines | |
| - name: Run Nanopore Nanopolish with metadata | |
| run: .github/scripts/test_nml_nanopore_nanopolish.sh | |
| - name: Run Nanopore Nanopolish with no metadata | |
| run: .github/scripts/test_nml_nanopore_nanopolish.sh --no_metadata | |
| - name: Run Nanopore Medaka with metadata | |
| run: .github/scripts/test_nml_nanopore_medaka.sh | |
| - name: Run Nanopore Medaka flat | |
| run: .github/scripts/test_nml_nanopore_medaka_flat.sh | |
| - name: Done Pipelines | |
| run: echo "Done running pipelines" |