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| --- | ||
| name: Issue template | ||
| about: Template to report an issue | ||
| title: '' | ||
| labels: '' | ||
| assignees: priesgo | ||
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| --- | ||
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| **Describe the issue** | ||
| A clear and concise description of what the bug is. | ||
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| **To Reproduce** | ||
| Steps to reproduce the behavior. | ||
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| **Expected behavior** | ||
| A clear and concise description of what you expected to happen. | ||
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| **Screenshots** | ||
| If applicable, add screenshots to help explain your problem. | ||
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| **Additional context** | ||
| Add any other context about the problem here. |
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| name: Automated tests | ||
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| on: [push] | ||
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| jobs: | ||
| test: | ||
| runs-on: ubuntu-20.04 | ||
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| steps: | ||
| - uses: actions/checkout@v2 | ||
| - uses: actions/setup-java@v2 | ||
| with: | ||
| distribution: 'zulu' # See 'Supported distributions' for available options | ||
| java-version: '11' | ||
| - uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| auto-update-conda: true | ||
| channels: defaults,conda-forge,bioconda | ||
| - name: Install dependencies | ||
| run: | | ||
| apt-get update && apt-get --assume-yes install wget make procps software-properties-common | ||
| wget -qO- https://get.nextflow.io | bash && cp nextflow /usr/local/bin/nextflow | ||
| conda update conda | ||
| - name: Cache conda environments | ||
| uses: actions/cache@v2 | ||
| with: | ||
| path: | | ||
| /home/runner/work/tronflow-bam-preprocessing/tronflow-bam-preprocessing/work/conda | ||
| key: ${{ runner.os }}-tronflow-bam-preprocessing | ||
| - name: Run tests | ||
| run: | | ||
| export NXF_VER=22.04.5 | ||
| make |
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,56 +1,20 @@ | ||
| all : clean test check | ||
| all : clean test | ||
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| clean: | ||
| rm -rf output | ||
| rm -f .nextflow.log* | ||
| rm -rf .nextflow* | ||
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| test: | ||
| nextflow main.nf --help | ||
| nextflow main.nf -profile test,conda --output output/test1 | ||
| nextflow main.nf -profile test,conda --skip_bqsr --output output/test2 | ||
| nextflow main.nf -profile test,conda --skip_realignment --output output/test3 | ||
| nextflow main.nf -profile test,conda --skip_deduplication --output output/test4 | ||
| nextflow main.nf -profile test,conda --output output/test5 --skip_deduplication --skip_bqsr --skip_metrics --known_indels1 false --known_indels2 false | ||
| nextflow main.nf -profile test,conda --output output/test6 --intervals false --skip_deduplication --skip_bqsr --skip_realignment | ||
| nextflow main.nf -profile test,conda --output output/test7 --skip_bqsr --skip_realignment | ||
| nextflow main.nf -profile test,conda --output output/test8 --collect_hs_metrics_min_base_quality 10 --collect_hs_metrics_min_mapping_quality 10 --remove_duplicates false --skip_bqsr --skip_realignment | ||
| nextflow main.nf -profile test,conda --output output/test9 --skip_deduplication --skip_bqsr --skip_realignment --input_files false --input_bam test_data/TESTX_S1_L001.bam | ||
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| check: | ||
| test -s output/test1/sample1/TESTX_S1_L001.preprocessed.bam || { echo "Missing test 1 output file!"; exit 1; } | ||
| test -s output/test1/sample1/TESTX_S1_L001.preprocessed.bai || { echo "Missing test 1 output file!"; exit 1; } | ||
| test -s output/test1/sample2/TESTX_S1_L002.preprocessed.bam || { echo "Missing test 1 output file!"; exit 1; } | ||
| test -s output/test1/sample2/TESTX_S1_L002.preprocessed.bai || { echo "Missing test 1 output file!"; exit 1; } | ||
| test -s output/test2/sample1/TESTX_S1_L001.preprocessed.bam || { echo "Missing test 2 output file!"; exit 1; } | ||
| test -s output/test2/sample1/TESTX_S1_L001.preprocessed.bai || { echo "Missing test 2 output file!"; exit 1; } | ||
| test -s output/test2/sample2/TESTX_S1_L002.preprocessed.bam || { echo "Missing test 2 output file!"; exit 1; } | ||
| test -s output/test2/sample2/TESTX_S1_L002.preprocessed.bai || { echo "Missing test 2 output file!"; exit 1; } | ||
| test -s output/test3/sample1/TESTX_S1_L001.preprocessed.bam || { echo "Missing test 3 output file!"; exit 1; } | ||
| test -s output/test3/sample1/TESTX_S1_L001.preprocessed.bai || { echo "Missing test 3 output file!"; exit 1; } | ||
| test -s output/test3/sample2/TESTX_S1_L002.preprocessed.bam || { echo "Missing test 3 output file!"; exit 1; } | ||
| test -s output/test3/sample2/TESTX_S1_L002.preprocessed.bai || { echo "Missing test 3 output file!"; exit 1; } | ||
| test -s output/test4/sample1/TESTX_S1_L001.preprocessed.bam || { echo "Missing test 4 output file!"; exit 1; } | ||
| test -s output/test4/sample1/TESTX_S1_L001.preprocessed.bai || { echo "Missing test 4 output file!"; exit 1; } | ||
| test -s output/test4/sample2/TESTX_S1_L002.preprocessed.bam || { echo "Missing test 4 output file!"; exit 1; } | ||
| test -s output/test4/sample2/TESTX_S1_L002.preprocessed.bai || { echo "Missing test 4 output file!"; exit 1; } | ||
| test -s output/test5/sample1/TESTX_S1_L001.preprocessed.bam || { echo "Missing test 5 output file!"; exit 1; } | ||
| test -s output/test5/sample1/TESTX_S1_L001.preprocessed.bai || { echo "Missing test 5 output file!"; exit 1; } | ||
| test -s output/test5/sample2/TESTX_S1_L002.preprocessed.bam || { echo "Missing test 5 output file!"; exit 1; } | ||
| test -s output/test5/sample2/TESTX_S1_L002.preprocessed.bai || { echo "Missing test 5 output file!"; exit 1; } | ||
| test -s output/test6/sample1/TESTX_S1_L001.preprocessed.bam || { echo "Missing test 6 output file!"; exit 1; } | ||
| test -s output/test6/sample1/TESTX_S1_L001.preprocessed.bai || { echo "Missing test 6 output file!"; exit 1; } | ||
| test -s output/test6/sample2/TESTX_S1_L002.preprocessed.bam || { echo "Missing test 6 output file!"; exit 1; } | ||
| test -s output/test6/sample2/TESTX_S1_L002.preprocessed.bai || { echo "Missing test 6 output file!"; exit 1; } | ||
| test -s output/test7/sample1/TESTX_S1_L001.preprocessed.bam || { echo "Missing test 7 output file!"; exit 1; } | ||
| test -s output/test7/sample1/TESTX_S1_L001.preprocessed.bai || { echo "Missing test 7 output file!"; exit 1; } | ||
| test -s output/test7/sample2/TESTX_S1_L002.preprocessed.bam || { echo "Missing test 7 output file!"; exit 1; } | ||
| test -s output/test7/sample2/TESTX_S1_L002.preprocessed.bai || { echo "Missing test 7 output file!"; exit 1; } | ||
| test -s output/test8/sample1/TESTX_S1_L001.preprocessed.bam || { echo "Missing test 8 output file!"; exit 1; } | ||
| test -s output/test8/sample1/TESTX_S1_L001.preprocessed.bai || { echo "Missing test 8 output file!"; exit 1; } | ||
| test -s output/test8/sample1/metrics/TESTX_S1_L001.prepared.dedup.hs_metrics.txt || { echo "Missing test 8 output file!"; exit 1; } | ||
| test -s output/test8/sample1/metrics/TESTX_S1_L001.prepared.dedup_metrics.txt || { echo "Missing test 8 output file!"; exit 1; } | ||
| test -s output/test8/sample2/TESTX_S1_L002.preprocessed.bam || { echo "Missing test 8 output file!"; exit 1; } | ||
| test -s output/test8/sample2/TESTX_S1_L002.preprocessed.bai || { echo "Missing test 8 output file!"; exit 1; } | ||
| test -s output/test9/TESTX_S1_L001/TESTX_S1_L001.preprocessed.bam || { echo "Missing test 9 output file!"; exit 1; } | ||
| test -s output/test9/TESTX_S1_L001/TESTX_S1_L001.preprocessed.bai || { echo "Missing test 9 output file!"; exit 1; } | ||
| bash tests/test_00.sh | ||
| bash tests/test_01.sh | ||
| bash tests/test_02.sh | ||
| bash tests/test_03.sh | ||
| bash tests/test_04.sh | ||
| bash tests/test_05.sh | ||
| bash tests/test_06.sh | ||
| bash tests/test_07.sh | ||
| bash tests/test_08.sh | ||
| bash tests/test_09.sh | ||
| bash tests/test_10.sh | ||
| bash tests/test_11.sh |
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