adding filter_and_trim files to output #36
Workflow file for this run
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| name: Run pipeline tests on PRs | |
| on: [push, pull_request] | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/nhoffman/dada2-nf:latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-java@v2 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '17' | |
| - run: | | |
| cd /usr/local/bin/ | |
| wget -qO - https://github.com/nextflow-io/nextflow/releases/download/v22.10.8/nextflow | bash | |
| - run: nextflow -quiet run main.nf -params-file test/minimal/params.json -without-docker -profile local | |
| - run: nextflow -quiet run main.nf -params-file test/its/params.json -without-docker -profile local | |
| - run: nextflow -quiet run main.nf -params-file test/noindex/params.json -without-docker -profile local | |
| - run: nextflow -quiet run main.nf -params-file test/single/cmsearch/params.json -without-docker -profile local | |
| - run: nextflow -quiet run main.nf -params-file test/single/vsearch/params.json -without-docker -profile local | |
| - run: nextflow -quiet run main.nf -params-file test/minimal/params.json -without-docker -profile local --manifest test/minimal/manifest.csv | |
| - run: nextflow -quiet run main.nf -params-file test/its/params.json -without-docker -profile local --manifest test/its/manifest.csv | |
| - run: nextflow -quiet run main.nf -params-file test/noindex/params.json -without-docker -profile local --manifest test/noindex/manifest.csv | |
| - run: nextflow -quiet run main.nf -params-file test/single/cmsearch/params.json -without-docker -profile local --manifest test/single/manifest.csv | |
| - run: nextflow -quiet run main.nf -params-file test/single/vsearch/params.json -without-docker -profile local --manifest test/single/manifest.csv | |
| - run: | | |
| cd test/ungs/ | |
| ./test_combine_svs.sh |