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c1eb9cce44
* Trimmomatic main only first draft * Add test files * SE PE Adjustment * Remove extra reads input * chore: Remove TODOs * Apply suggestions from code review Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * fix(trimmomatic): Handle SE output correctly Since there's never going to be unpaired reads for SE reads we can get away with it for SE * fix(trimmomatic): Use correct elvis operator to handle logic * fix(trimmomatic): Add hack to work with SE and PE reads * Update test.yml * use the PE and SE trimming correctly * Made user set adaptors * Add documentation * test(trimmomatic): Add files to pytest_modules * test(trimmomatic): Update name of failing test Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
26 lines
1.2 KiB
YAML
26 lines
1.2 KiB
YAML
- name: trimmomatic single-end
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command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_single_end -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config
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tags:
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- "trimmomatic"
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files:
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- path: "output/trimmomatic/test.SE.paired.trim.fastq.gz"
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- path: "output/trimmomatic/test.log"
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md5sum: e4c3f619e9b0e26847f8f3e3d9af319b
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- name: trimmomatic paired-end
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command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config
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tags:
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- "trimmomatic"
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files:
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- path: "output/trimmomatic/test.log"
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md5sum: 9629761761a34576b3484bf4174f681f
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- path: "output/trimmomatic/test.paired.trim_1.fastq.gz"
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- path: "output/trimmomatic/test.unpaired.trim_1.fastq.gz"
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- path: "output/trimmomatic/test.paired.trim_2.fastq.gz"
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- path: "output/trimmomatic/test.unpaired.trim_2.fastq.gz"
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- name: trimmomatic no adapter specified
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command: nextflow run ./tests/modules/trimmomatic -entry test_trimmomatic_no_adaptor -c ./tests/config/nextflow.config -c ./tests/modules/trimmomatic/nextflow.config
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tags:
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- "trimmomatic"
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exit_code: 1
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