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Merge pull request #5 from StefaanVerwimp/new_serotypes #43

Merge pull request #5 from StefaanVerwimp/new_serotypes

Merge pull request #5 from StefaanVerwimp/new_serotypes #43

Workflow file for this run

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
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