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pangolin-ubuntu

Update data_compatibility.csv #681

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Update data_compatibility.csv

Update data_compatibility.csv #681

Workflow file for this run

.github/workflows/pangolin.yml at 5a67153
name: pangolin-ubuntu
on: [push, pull_request]
defaults:
run:
shell: bash -l {0}
jobs:
run_pangolin_test:
name: Pangolin test on ${{ matrix.os }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ["ubuntu-latest"]
steps:
- uses: actions/checkout@v2
- uses: conda-incubator/setup-miniconda@v2
with:
environment-file: environment.yml
activate-environment: pangolin
channels: conda-forge,bioconda,defaults
conda-version: "23.5.0"
mamba-version: "*"
- name: Install pangolin
run: pip install -e .
- name: Check pangolin version
run: pangolin --version
- name: Run pangolin with test data
run: pangolin pangolin/test/test_seqs.fasta 2>&1 | tee pangolin.log
- name: Compare assigned lineages (first two columns only) with expected values
run: cut -d, -f1,2 lineage_report.csv | diff - pangolin/test/test_seqs.assignments.csv
- name: Run pangolin with test zip data
run: pangolin pangolin/test/test_seqs.fasta.gz 2>&1 | tee pangolin_zip.log
- name: Run pangolin with test all cache data
run: pangolin pangolin/test/all_bad_seqs.fasta 2>&1 | tee pangolin_all_bad.log
- name: Run pangolin with test all bad data
run: pangolin pangolin/test/all_hash.fasta 2>&1 | tee pangolin_cache.log
- name: Run pangolin usher with test data
run: pangolin --analysis-mode usher pangolin/test/test_seqs.fasta 2>&1 | tee pangolin_usher.log
- name: Run pangolin accurate with test data
run: pangolin --analysis-mode accurate pangolin/test/test_seqs.fasta 2>&1 | tee pangolin_accurate.log
- name: Run pangolin with outdir and outfile
run: pangolin pangolin/test/test_seqs.fasta -o my_test --outfile pangolin_out.txt 2>&1 | tee pangolin_outdir_outfile.log
- name: Run pangolin with out alignment
run: pangolin pangolin/test/test_seqs.fasta --alignment --alignment-file my_alignment.fasta 2>&1 | tee pangolin_alignment.log
- name: Run pangolin aliases
run: pangolin --aliases 2>&1 | tee pangolin_alias.log
- name: Run pangolin all versions
run: pangolin --all-versions 2>&1 | tee pangolin_versions.log
- name: Run pangolin skip designation cache
run: pangolin pangolin/test/test_seqs.fasta --skip-designation-cache 2>&1 | tee pangolin_no_cache.log
- name: Run pangolin update
run: pangolin --update 2>&1 | tee pangolin_update.log
- name: Run pangolin update data
run: pangolin --update-data 2>&1 | tee pangolin_update_data.log
- name: Run pangolin verbose mode
run: pangolin --verbose pangolin/test/test_seqs.fasta 2>&1 | tee pangolin_verbose.log
- name: Add assignment cache
run: pangolin --add-assignment-cache
- name: remove assignment cache
run: pip uninstall -y pangolin-assignment