perf: update to varlociraptor 8.4 #2463
Workflow file for this run
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name: Tests | |
on: | |
push: | |
branches: | |
- master | |
pull_request: | |
branches: | |
- "*" | |
jobs: | |
Cancel-previous-jobs: | |
runs-on: ubuntu-latest | |
if: github.ref != 'refs/heads/master' | |
steps: | |
- uses: khan/[email protected] | |
with: | |
workflows: "main.yml" | |
env: | |
GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}" | |
Formatting: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Formatting | |
uses: github/[email protected] | |
env: | |
VALIDATE_ALL_CODEBASE: false | |
DEFAULT_BRANCH: master | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
FILTER_REGEX_EXCLUDE: CHANGELOG.md | |
VALIDATE_SNAKEMAKE_SNAKEFMT: true | |
VALIDATE_PYTHON_BLACK: true | |
VALIDATE_MARKDOWN: true | |
Linting: | |
runs-on: ubuntu-latest | |
env: | |
GISAID_API_TOKEN: ${{ secrets.GISAID_API_TOKEN }} | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Lint workflow | |
uses: snakemake/[email protected] | |
with: | |
directory: . | |
snakefile: workflow/Snakefile | |
stagein: mamba install -n snakemake -c conda-forge peppy | |
args: "--lint" | |
# pre-commit action currently fails: | |
# https://github.com/IKIM-Essen/uncovar/actions/runs/4304753941/jobs/7506225198#step:4:115 | |
# revisit when new pre-commit release >3.0.0 is out | |
# Pre-Commit: | |
# runs-on: ubuntu-latest | |
# if: github.ref != 'refs/heads/master' | |
# steps: | |
# - uses: actions/checkout@v2 | |
# - uses: actions/setup-python@v4 | |
# - uses: pre-commit/[email protected] | |
Technology-Tests: | |
runs-on: ubuntu-latest | |
env: | |
GISAID_API_TOKEN: ${{ secrets.GISAID_API_TOKEN }} | |
needs: | |
- Formatting | |
- Linting | |
#- Pre-Commit | |
strategy: | |
matrix: | |
rule: [all, all -npr] | |
# disable ont actions | |
# technology: [all, illumina, ont, ion] | |
technology: [all, illumina, ion] | |
seq_method: [shotgun, amplicon] | |
steps: | |
- uses: actions/checkout@v2 | |
# android - will release about 10 GB if you don't need Android | |
# dotnet - will release about 20 GB if you don't need .NET | |
- name: Free up some disk sapce | |
run: | | |
sudo rm -rf /usr/local/lib/android | |
sudo rm -rf /usr/share/dotnet | |
- name: Prepare test data for all technologies | |
if: steps.test-data.outputs.cache-hit != true && (startsWith(matrix.rule, 'all') && matrix.technology == 'all' || matrix.rule == 'compare_assemblers') | |
run: | | |
if [[ "${{ matrix.seq_method }}" = "shotgun" ]] ; then export AMPLICON=0; else export AMPLICON=1; fi | |
mkdir -p .tests/data | |
curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/B.1.1.7.reads.1.fastq.gz > .tests/data/B117.1.fastq.gz | |
curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/B.1.1.7.reads.1.fastq.gz > .tests/data/B117.2.fastq.gz | |
curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/ERR5745913.fastq.gz > .tests/data/ion_reads.fastq.gz | |
echo sample_name,fq1,fq2,date,is_amplicon_data,technology > .tests/config/pep/samples.csv | |
echo illumina-test,data/B117.1.fastq.gz,data/B117.2.fastq.gz,2022-01-01,$AMPLICON,illumina >> .tests/config/pep/samples.csv | |
echo ion-test,data/ion_reads.fastq.gz,,2022-01-01,$AMPLICON,ion >> .tests/config/pep/samples.csv | |
- name: Prepare test data for Illumina | |
if: steps.test-data.outputs.cache-hit != true && (startsWith(matrix.rule, 'all') && matrix.technology == 'illumina' || matrix.rule == 'compare_assemblers') | |
run: | | |
if [[ "${{ matrix.seq_method }}" = "shotgun" ]] ; then export AMPLICON=0; else export AMPLICON=1; fi | |
mkdir -p .tests/data | |
curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/B.1.1.7.reads.1.fastq.gz > .tests/data/B117.1.fastq.gz | |
curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/B.1.1.7.reads.1.fastq.gz > .tests/data/B117.2.fastq.gz | |
echo sample_name,fq1,fq2,date,is_amplicon_data,technology > .tests/config/pep/samples.csv | |
echo illumina-test,data/B117.1.fastq.gz,data/B117.2.fastq.gz,2022-01-01,$AMPLICON,illumina >> .tests/config/pep/samples.csv | |
# - name: Prepare test data for Oxford Nanopore | |
# if: steps.test-data.outputs.cache-hit != true && (startsWith(matrix.rule, 'all') && matrix.technology == 'ont' || matrix.rule == 'compare_assemblers') | |
# run: | | |
# if [[ "${{ matrix.seq_method }}" = "shotgun" ]] ; then export AMPLICON=0; else export AMPLICON=1; fi | |
# mkdir -p .tests/data | |
# curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/ont_reads.fastq.gz > .tests/data/ont_reads.fastq.gz | |
# echo sample_name,fq1,date,is_amplicon_data,technology > .tests/config/pep/samples.csv | |
# echo ont-test,data/ont_reads.fastq.gz,2022-01-01,$AMPLICON,ont >> .tests/config/pep/samples.csv | |
- name: Prepare test data for Ion Torrent | |
if: steps.test-data.outputs.cache-hit != true && (startsWith(matrix.rule, 'all') && matrix.technology == 'ion' || matrix.rule == 'compare_assemblers') | |
run: | | |
if [[ "${{ matrix.seq_method }}" = "shotgun" ]] ; then export AMPLICON=0; else export AMPLICON=1; fi | |
mkdir -p .tests/data | |
curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/ERR5745913.fastq.gz > .tests/data/ion_reads.fastq.gz | |
echo sample_name,fq1,date,is_amplicon_data,technology > .tests/config/pep/samples.csv | |
echo ion-test,data/ion_reads.fastq.gz,2022-01-01,$AMPLICON,ion >> .tests/config/pep/samples.csv | |
- name: Use smaller reference files for testing | |
if: steps.test-resources.outputs.cache-hit != true | |
run: | | |
# mkdir -p .tests/resources/minikraken-8GB | |
# curl -SL https://github.com/thomasbtf/small-kraken-db/raw/master/human_k2db.tar.gz | tar zxvf - -C .tests/resources/minikraken-8GB --strip 1 | |
mkdir -p .tests/resources/genomes | |
curl -SL "https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=BA000005.3&db=nuccore&report=fasta" | gzip -c > .tests/resources/genomes/human-genome.fna.gz | |
- name: Simulate GISAID download | |
run: | | |
mkdir -p .tests/results/benchmarking/tables | |
echo -e "resources/genomes/B.1.1.7.fasta\nresources/genomes/B.1.351.fasta" > .tests/results/benchmarking/tables/strain-genomes.txt | |
mkdir -p .tests/resources/genomes | |
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=MZ314997.1&rettype=fasta" | sed '$ d' > .tests/resources/genomes/B.1.1.7.fasta | |
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=MZ314998.1&rettype=fasta" | sed '$ d' > .tests/resources/genomes/B.1.351.fasta | |
- name: Test rule ${{ matrix.rule }} on ${{ matrix.technology }} ${{ matrix.seq_method }} data | |
uses: snakemake/[email protected] | |
with: | |
directory: .tests | |
snakefile: workflow/Snakefile | |
args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}" | |
- name: Test report | |
uses: snakemake/[email protected] | |
if: startsWith(matrix.rule, 'all -npr') != true | |
with: | |
directory: .tests | |
snakefile: workflow/Snakefile | |
args: "${{ matrix.rule }} --report report.zip" | |
- name: Upload report | |
uses: actions/upload-artifact@v3 | |
if: matrix.technology == 'all' && matrix.rule != 'all -npr' | |
with: | |
name: report-rule-${{ matrix.rule }}-${{ matrix.technology }}-${{ matrix.seq_method }} | |
path: .tests/results/patient-reports/2022-01-01.zip | |
- name: Upload logs | |
uses: actions/upload-artifact@v3 | |
if: matrix.technology == 'all' && matrix.rule != 'all -npr' | |
with: | |
name: log-rule-${{ matrix.rule }}-technology-${{ matrix.technology }} | |
path: .tests/logs/ | |
- name: Change permissions for caching | |
run: sudo chmod -R 755 .tests/.snakemake/conda | |
- name: Print disk space | |
run: sudo df -h | |
Benchmarks-Tests: | |
runs-on: ubuntu-latest | |
env: | |
GISAID_API_TOKEN: ${{ secrets.GISAID_API_TOKEN }} | |
needs: | |
- Formatting | |
- Linting | |
#- Pre-Commit | |
strategy: | |
matrix: | |
rule: | |
[ | |
benchmark_strain_calling, | |
benchmark_assembly, | |
benchmark_mixtures, | |
benchmark_non_sars_cov_2, | |
benchmark_reads, | |
compare_assemblers, | |
] | |
# generate_test_cases, | |
steps: | |
- uses: actions/checkout@v2 | |
# - name: Cache conda dependencies | |
# uses: actions/cache@v2 | |
# with: | |
# path: | | |
# .tests/.snakemake/conda | |
# key: benchmarks-${{ runner.os }}-${{ matrix.rule }}-${{ matrix.technology }}-${{ matrix.seq_method }}-${{ hashFiles('*.tests/.snakemake/conda/*.yaml') }} | |
# TODO caches are currently completely misleading, as they lead to certain files becoming present on disk which might | |
# then hide failures that would otherwise be seen. | |
# - name: Get date | |
# id: get-date | |
# run: | | |
# echo "::set-output name=date::$(/bin/date -u "+%Y%m%d")" | |
# shell: bash | |
# - name: Cache resources | |
# id: test-resources | |
# uses: actions/cache@v2 | |
# with: | |
# path: | | |
# .tests/resources/minikraken-8GB | |
# .tests/resources/genomes/human-genome.fna.gz | |
# key: ${{ runner.os }}-test-resources-${{ steps.get-date.outputs.date }}-${{ hashFiles('**.tests/resources**taxo.k2d') }} | |
# restore-keys: | | |
# ${{ runner.os }}-test-resources-${{ steps.get-date.outputs.date }}- | |
# ${{ runner.os }}-test-resources- | |
# - name: Cache results | |
# if: startsWith(matrix.rule, 'all') | |
# id: test-results | |
# uses: actions/cache@v2 | |
# with: | |
# path: | | |
# .tests/results | |
# key: ${{ runner.os }}-results-${{ steps.get-date.outputs.date }}-${{ hashFiles('**results/2021-02-01/qc/multiqc.html') }} | |
# restore-keys: | | |
# ${{ runner.os }}-results-${{ steps.get-date.outputs.date }}- | |
# ${{ runner.os }}-results- | |
# - name: Cache data | |
# if: startsWith(matrix.rule, 'all') | |
# id: test-data | |
# uses: actions/cache@v2 | |
# with: | |
# path: | | |
# .tests/data | |
# key: ${{ runner.os }}-test-data-${{ steps.get-date.outputs.date }}-${{ hashFiles('**.tests/data/*.fastq.gz') }} | |
# restore-keys: | | |
# ${{ runner.os }}-test-data-${{ steps.get-date.outputs.date }}- | |
# ${{ runner.os }}-test-data- | |
# - name: Cache benchmark data | |
# if: startsWith(matrix.rule, 'all') != true | |
# id: benchmark-data | |
# uses: actions/cache@v2 | |
# with: | |
# path: | | |
# .tests/resources/benchmarking | |
# key: ${{ runner.os }}-benchmark-data-${{ steps.get-date.outputs.date }}-${{ hashFiles('**.tests/resources/benchmarking/**/reads.1.fastq.gz') }} | |
# restore-keys: | | |
# ${{ runner.os }}-benchmark-data-${{ steps.get-date.outputs.date }}- | |
# ${{ runner.os }}-benchmark-data- | |
# - name: Cache test dependencies | |
# if: startsWith(matrix.rule, 'all') | |
# id: test-dependencies | |
# uses: actions/cache@v2 | |
# with: | |
# path: | | |
# .tests/.snakemake/conda | |
# key: ${{ runner.os }}-sars-cov-test-dependencies-${{ steps.get-date.outputs.date }}-${{ hashFiles('*.tests/.snakemake/conda/*.yaml') }} | |
# restore-keys: | | |
# ${{ runner.os }}-sars-cov-test-dependencies-${{ steps.get-date.outputs.date }}- | |
# ${{ runner.os }}-sars-cov-test-dependencies- | |
# - name: Cache benchmark dependencies | |
# if: startsWith(matrix.rule, 'all') != true | |
# id: benchmark-dependencies | |
# uses: actions/cache@v2 | |
# with: | |
# path: | | |
# .tests/.snakemake/conda | |
# key: ${{ runner.os }}-sars-cov-benchmark-dependencies-${{ steps.get-date.outputs.date }}-${{ hashFiles('*.tests/.snakemake/conda/*.yaml') }} | |
# restore-keys: | | |
# ${{ runner.os }}-sars-cov-benchmark-dependencies-${{ steps.get-date.outputs.date }}- | |
# ${{ runner.os }}-sars-cov-benchmark-dependencies- | |
- name: Prepare test data | |
if: matrix.rule == 'generate_test_cases' | |
run: | | |
mkdir -p .tests/data | |
curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/B.1.1.7.reads.1.fastq.gz > .tests/data/B117.1.fastq.gz | |
curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/B.1.1.7.reads.1.fastq.gz > .tests/data/B117.2.fastq.gz | |
curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/ont_reads.fastq.gz > .tests/data/ont_reads.fastq.gz | |
echo sample_name,fq1,fq2,date,is_amplicon_data,technology,test_case > .tests/config/pep/samples.csv | |
echo illumina-test,data/B117.1.fastq.gz,data/B117.2.fastq.gz,2022-01-01,1,illumina,case >> .tests/config/pep/samples.csv | |
echo ont-test,data/ont_reads.fastq.gz,,2022-01-01,1,ont,case >> .tests/config/pep/samples.csv | |
- name: Prepare test data | |
if: matrix.rule != 'generate_test_cases' | |
run: | | |
mkdir -p .tests/data | |
curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/B.1.1.7.reads.1.fastq.gz > .tests/data/B117.1.fastq.gz | |
curl -L https://github.com/thomasbtf/small-kraken-db/raw/master/B.1.1.7.reads.1.fastq.gz > .tests/data/B117.2.fastq.gz | |
echo sample_name,fq1,fq2,date,is_amplicon_data,technology > .tests/config/pep/samples.csv | |
echo illumina-test,data/B117.1.fastq.gz,data/B117.2.fastq.gz,2022-01-01,0,illumina >> .tests/config/pep/samples.csv | |
- name: Use smaller reference files for testing | |
if: steps.test-resources.outputs.cache-hit != true | |
run: | | |
# mkdir -p .tests/resources/minikraken-8GB | |
# curl -SL https://github.com/thomasbtf/small-kraken-db/raw/master/human_k2db.tar.gz | tar zxvf - -C .tests/resources/minikraken-8GB --strip 1 | |
mkdir -p .tests/resources/genomes | |
curl -SL "https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=BA000005.3&db=nuccore&report=fasta" | gzip -c > .tests/resources/genomes/human-genome.fna.gz | |
- name: Simulate GISAID download | |
run: | | |
mkdir -p .tests/results/benchmarking/tables | |
echo -e "resources/genomes/B.1.1.7.fasta\nresources/genomes/B.1.351.fasta" > .tests/results/benchmarking/tables/strain-genomes.txt | |
mkdir -p .tests/resources/genomes | |
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=MZ314997.1&rettype=fasta" | sed '$ d' > .tests/resources/genomes/B.1.1.7.fasta | |
curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=MZ314998.1&rettype=fasta" | sed '$ d' > .tests/resources/genomes/B.1.351.fasta | |
- name: Test rule ${{ matrix.rule }} | |
uses: snakemake/[email protected] | |
with: | |
directory: .tests | |
snakefile: workflow/Snakefile | |
args: "-pr --use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba ${{ matrix.rule }}" | |
- name: Test report | |
uses: snakemake/[email protected] | |
if: startsWith(matrix.rule, 'all -npr') != true | |
with: | |
directory: .tests | |
snakefile: workflow/Snakefile | |
args: "${{ matrix.rule }} --report report.zip" | |
# - name: Upload report | |
# uses: actions/upload-artifact@v3 | |
# with: | |
# name: report-rule-${{ matrix.rule }} | |
# path: .tests/results/patient-reports/2022-01-01.zip | |
- name: Upload logs | |
uses: actions/upload-artifact@v3 | |
with: | |
name: log-rule-${{ matrix.rule }} | |
path: .tests/logs/ | |
# - name: Unit test | |
# args: "--generate-unit-tests" | |
# - name: Test workflow (singularity) | |
# args: "--use-conda --use-singularity --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba" | |
# - name: Test input changes | |
# args: "--use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba -R `snakemake --list-input-changes`" | |
# - name: Test code changes | |
# args: "--use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba -R `snakemake --list-code-changes`" | |
# - name: Test params changes | |
# args: "--use-conda --show-failed-logs --cores 2 --resources ncbi_api_requests=1 --conda-cleanup-pkgs cache --conda-frontend mamba -R `snakemake --list-params-changes`" | |
- name: Check strain calling benchmark | |
if: matrix.rule == 'benchmark_strain_calling' | |
run: | | |
cat .tests/results/benchmarking/strain-calling.csv | |
if (tail -n+2 .tests/results/benchmarking/strain-calling.csv | grep mismatch > /dev/null) | |
then | |
echo "Strain calling failed in some cases (see above)." | |
exit 1 | |
else | |
echo "Strain calling was successful in all cases." | |
fi | |
- name: Check pseudoassembly benchmark | |
if: matrix.rule == 'benchmark_assembly' | |
run: | | |
cat .tests/results/benchmarking/assembly/pseudoassembly.csv | |
if [[ $(tail -1 .tests/results/benchmarking/assembly/pseudoassembly.csv) < 0.95 ]] | |
then | |
echo "Pseudoassembly benchmarking failed. There is at least one assembly where the contigs do not cover 95% of the original sequence (see above)." | |
exit 1 | |
else | |
echo "Pseudoassembly was successful." | |
fi | |
- name: Check assembly benchmark | |
if: matrix.rule == 'benchmark_assembly' | |
run: | | |
cat .tests/results/benchmarking/assembly/assembly.csv | |
if [[ $(tail -1 .tests/results/benchmarking/assembly/assembly.csv) < 0.8 ]] | |
then | |
echo "Assembly benchmarking failed. There is at least one assembly where the contigs do not cover 80% of the original sequence (see above)." | |
exit 1 | |
else | |
echo "Assembly was successful." | |
fi | |
- name: Print non-sars-cov-2 kallisto calls | |
if: matrix.rule == 'benchmark_non_sars_cov_2' | |
run: | | |
cat .tests/results/benchmarking/tables/strain-calls/non-cov2-*.strains.kallisto.tsv | |
- name: Test non-sars-cov-2 coronaviruses | |
if: matrix.rule == 'benchmark_non_sars_cov_2' | |
run: | | |
cat .tests/results/benchmarking/non-sars-cov-2.csv | |
if (cat .tests/results/benchmarking/non-sars-cov-2.csv | grep 'is sars-cov-2' > /dev/null) | |
then | |
echo "Workflow failed! A non-sars-cov-2 genome was identified as sars-cov-2 (see above)." | |
exit 1 | |
else | |
echo "Workflow sucessfully identified samples as non-sars-cov-2 in all cases." | |
fi | |
- name: Change permissions for caching | |
run: sudo chmod -R 755 .tests/.snakemake/conda | |
- name: Print disk space | |
run: sudo df -h |