update #1
Workflow file for this run
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| name: GOTTCHA2 Tests | |
| on: | |
| push: | |
| branches: [ main, develop ] | |
| pull_request: | |
| branches: [ main, develop ] | |
| workflow_dispatch: | |
| permissions: | |
| contents: read | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| functional-tests: | |
| name: GOTTCHA2 test (${{ matrix.python-version }}, ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 45 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.9", "3.11"] | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Conda environment | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| use-mamba: true | |
| activate-environment: gottcha2 | |
| environment-file: environment.yml | |
| python-version: ${{ matrix.python-version }} | |
| - name: Installation | |
| run: | | |
| set -euxo pipefail | |
| python -m pip install --upgrade pip | |
| python -m pip install --no-deps . | |
| gottcha2 profile --help | |
| - name: Prepare testing dataset | |
| working-directory: test | |
| run: | | |
| set -euxo pipefail | |
| tar -xzf gottcha2_database_Ebola_test.tar.gz | |
| - name: Run testing dataset - Backwards compatibility | |
| working-directory: test | |
| run: | | |
| set -euxo pipefail | |
| gottcha2.py -d gottcha2_database_test/gottcha_db.species.fna -t2 -i SRR12689945_1_1k.fastq.gz SRR12689945_2_1k.fastq.gz -o output | |
| grep 'Orthoebolavirus zairense' output/SRR12689945_1_1k.tsv | |
| - name: Run testing dataset - Basic profile tests | |
| working-directory: test | |
| run: | | |
| set -euxo pipefail | |
| gottcha2 profile -d gottcha2_database_test/gottcha_db.species.fna -i SRR12689945_1_1k.fastq.gz -o output | |
| gottcha2 profile -d gottcha2_database_test/gottcha_db.species.fna -i SRR12689945_1_1k.fastq.gz SRR12689945_2_1k.fastq.gz -o output | |
| grep 'Orthoebolavirus zairense' output/SRR12689945_1_1k.tsv | |
| - name: Run testing dataset - Advanced profile tests | |
| working-directory: test | |
| run: | | |
| set -euxo pipefail | |
| gottcha2 profile -d gottcha2_database_test/gottcha_db.species.fna -i gottcha2_database_test/gottcha_db.species.fna.gz -np -o output | |
| gottcha2 profile -d gottcha2_database_test/gottcha_db.species.fna -i SRR12689945_1_1k.fastq.gz -nc -o output | |
| gottcha2 profile -d gottcha2_database_test/gottcha_db.species.fna -b output/SRR12689945_1_1k.gottcha_species.bam -o output | |
| grep 'Orthoebolavirus zairense' output/SRR12689945_1_1k.tsv | |
| - name: Run testing dataset - Profile tests with additional options | |
| working-directory: test | |
| run: | | |
| set -euxo pipefail | |
| gottcha2 profile -d gottcha2_database_test/gottcha_db.species.fna -i SRR12689945_1_1k.fastq.gz -mi 0.9 -mf 0.9 -mg 100 -o output | |
| gottcha2 profile -d gottcha2_database_test/gottcha_db.species.fna -b output/SRR12689945_1_1k.gottcha_species.bam -sl gottcha2_database_test/aoi_list.txt -o output | |
| grep 'Orthoebolavirus zairense' output/SRR12689945_1_1k.tsv | |
| - name: Run testing dataset - ONT profile tests | |
| working-directory: test | |
| run: | | |
| set -euxo pipefail | |
| gottcha2 profile -d gottcha2_database_test/gottcha_db.species.fna -i SRR2016557_extract.fasta.gz -o output -np -er 0.05 | |
| grep 'Orthoebolavirus zairense' output/SRR2016557_extract.tsv | |
| - name: Run testing dataset - Profile with additional database options | |
| working-directory: test | |
| run: | | |
| set -euxo pipefail | |
| rm -rf output/SRR12689945_1_1k.tsv | |
| gottcha2 profile -d gottcha2_database_test/gottcha_db.species.fna -i SRR12689945_1_1k.fastq.gz -o output | |
| grep 'Orthoebolavirus zairense' output/SRR12689945_1_1k.tsv | |
| gottcha2 profile -d gottcha2_database_test/gottcha_db.species.fna.mmi -i SRR12689945_1_1k.fastq.gz -o output | |
| grep 'Orthoebolavirus zairense' output/SRR12689945_1_1k.tsv | |
| gottcha2 profile -d gottcha2_database_test -i SRR12689945_1_1k.fastq.gz -o output | |
| grep 'Orthoebolavirus zairense' output/SRR12689945_1_1k.tsv | |
| gottcha2 fast-profile -d gottcha2_database_test/gottcha_db.species.fna.syldb -i SRR12689945_1_1k.fastq.gz -o output | |
| grep 'Orthoebolavirus zairense' output/SRR12689945_1_1k.tsv | |
| gottcha2 fast-profile -d gottcha2_database_test -i SRR12689945_1_1k.fastq.gz -o output | |
| grep 'Orthoebolavirus zairense' output/SRR12689945_1_1k.tsv | |
| - name: Run testing dataset - fast-profile tests | |
| working-directory: test | |
| run: | | |
| set -euxo pipefail | |
| gottcha2 fast-profile -d gottcha2_database_test/gottcha_db.species.fna -i SRR12689945_1_1k.fastq.gz -o output | |
| grep 'Orthoebolavirus zairense' output/SRR12689945_1_1k.tsv | |
| gottcha2 fast-profile -d gottcha2_database_test/gottcha_db.species.fna -i SRR2016557_extract.fasta.gz -o output -np -er 0.05 | |
| grep 'Orthoebolavirus zairense' output/SRR2016557_extract.tsv | |
| - name: Test extract functionality - Simple extraction | |
| working-directory: test | |
| run: | | |
| set -euxo pipefail | |
| gottcha2 profile -d gottcha2_database_test/gottcha_db.species.fna -i SRR12689945_1_1k.fastq.gz -mi 0.9 -mf 0.9 -mg 100 -o output | |
| gottcha2 extract -d gottcha2_database_test/gottcha_db.species.fna -e 3052462 -b output/SRR12689945_1_1k.gottcha_species.bam -p test_ext -o output | |
| count_tsv=$(grep "3052462" output/SRR12689945_1_1k.tsv | cut -f4) | |
| grep -c '>' output/test_ext.extract.fasta | grep $count_tsv | |
| - name: Test extract functionality - Additional extraction options | |
| working-directory: test | |
| run: | | |
| set -euxo pipefail | |
| gottcha2 extract -d gottcha2_database_test/gottcha_db.species.fna -e 3052462:10:fastq -b output/SRR12689945_1_1k.gottcha_species.bam -p test_ext1 -o output | |
| wc -l output/test_ext1.extract.fastq | grep 40 | |
| gottcha2 extract -d gottcha2_database_test/gottcha_db.species.fna -ef -eo -b output/SRR12689945_1_1k.gottcha_species.bam -p test_ext2 -o output | |
| wc -l output/test_ext2.extract.fasta | grep 280 | |
| - name: Run unittests | |
| run: | | |
| set -euxo pipefail | |
| python -m unittest discover test -v |