update default cutoffs #48
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| name: pasty-test | |
| on: | |
| push: | |
| branches: [ main, dev ] | |
| pull_request: | |
| branches: [ main, dev ] | |
| jobs: | |
| pasty-tests: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout rpetit3/pasty | |
| uses: actions/checkout@v2 | |
| - name: Setup miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: pasty | |
| auto-activate-base: false | |
| - name: Setup pasty Environment | |
| run: | | |
| conda install -y -c conda-forge -c bioconda 'camlhmp>=0.3.1' | |
| - name: Environment Information | |
| run: uname -a && env | |
| - name: Test pasty basics | |
| run: | | |
| echo "Testing patsy" | |
| bin/pasty --version | |
| bin/pasty --help | |
| - name: Test patsy | |
| run: | | |
| echo "O1-GCF_001420225" | |
| bin/pasty --input test/data/O1-GCF_001420225.fna.gz --prefix O1-GCF_001420225 | |
| cat O1-GCF_001420225.tsv | |
| cat O1-GCF_001420225.details.tsv | |
| echo "O2-GCF_001420185" | |
| bin/pasty --input test/data/O2-GCF_001420185.fna.gz --prefix O2-GCF_001420185 --outdir O2 | |
| cat O2/O2-GCF_001420185.tsv | |
| cat O2/O2-GCF_001420185.details.tsv | |
| echo "O3-GCF_001420205" | |
| bin/pasty --input test/data/O3-GCF_001420205.fna.gz --prefix O3-GCF_001420205 --outdir O3 | |
| cat O3/O3-GCF_001420205.tsv | |
| cat O3/O3-GCF_001420205.details.tsv | |
| echo "O4-GCF_001420245" | |
| bin/pasty --input test/data/O4-GCF_001420245.fna.gz --prefix O4-GCF_001420245 --outdir O4 | |
| cat O4/O4-GCF_001420245.tsv | |
| cat O4/O4-GCF_001420245.details.tsv | |
| echo "O5-GCF_001420265" | |
| bin/pasty --input test/data/O5-GCF_001420265.fna.gz --prefix O5-GCF_001420265 --outdir O5 | |
| cat O5/O5-GCF_001420265.tsv | |
| cat O5/O5-GCF_001420265.details.tsv | |
| echo "O6-GCF_001444755" | |
| bin/pasty --input test/data/O6-GCF_001444755.fna.gz --prefix O6-GCF_001444755 | |
| cat O6-GCF_001444755.tsv | |
| cat O6-GCF_001444755.details.tsv | |
| echo "O7-GCF_001444745" | |
| bin/pasty --input test/data/O7-GCF_001444745.fna.gz --prefix O7-GCF_001444745 | |
| cat O7-GCF_001444745.tsv | |
| cat O7-GCF_001444745.details.tsv | |
| echo "O9-GCF_001444815" | |
| bin/pasty --input test/data/O9-GCF_001444815.fna.gz --prefix O9-GCF_001444815 | |
| cat O9-GCF_001444815.tsv | |
| cat O9-GCF_001444815.details.tsv | |
| echo "O10-GCF_001444835" | |
| bin/pasty --input test/data/O10-GCF_001444835.fna.gz --prefix O10-GCF_001444835 | |
| cat O10-GCF_001444835.tsv | |
| cat O10-GCF_001444835.details.tsv | |
| echo "O11-GCF_001444955" | |
| bin/pasty --input test/data/O11-GCF_001444955.fna.gz --prefix O11-GCF_001444955 | |
| cat O11-GCF_001444955.tsv | |
| cat O11-GCF_001444955.details.tsv | |
| echo "O12-GCF_001444975" | |
| bin/pasty --input test/data/O12-GCF_001444975.fna.gz --prefix O12-GCF_001444975 | |
| cat O12-GCF_001444975.tsv | |
| cat O12-GCF_001444975.details.tsv | |
| echo "O13-GCF_001444995" | |
| bin/pasty --input test/data/O13-GCF_001444995.fna.gz --prefix O13-GCF_001444995 | |
| cat O13-GCF_001444995.tsv | |
| cat O13-GCF_001444995.details.tsv | |
| bin/pasty --input test/data/O15-GCF_001444865.fna.gz --prefix O15-GCF_001444865 | |
| cat O15-GCF_001444865.tsv | |
| cat O15-GCF_001444865.details.tsv | |
| bin/pasty --input test/data/O17-GCF_001444915.fna.gz --prefix O17-GCF_001444915 | |
| cat O17-GCF_001444915.tsv | |
| cat O17-GCF_001444915.details.tsv | |
| echo "NT-GCF_000292685" | |
| bin/pasty --input test/data/NT-GCF_000292685.fna.gz --prefix NT-GCF_000292685 | |
| cat NT-GCF_000292685.tsv | |
| cat NT-GCF_000292685.details.tsv | |
| echo "not-a-fasta" | |
| bin/pasty --input test/data/not-a-fasta.fasta --prefix not-a-fasta | |
| cat not-a-fasta.tsv | |
| cat not-a-fasta.details.tsv | |
| echo "poor" | |
| bin/pasty --input test/data/poor.fasta --prefix poor --outdir poor | |
| cat poor/poor.tsv | |
| cat poor/poor.details.tsv |