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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>
53 lines
1.4 KiB
YAML
53 lines
1.4 KiB
YAML
name: "trimmomatic"
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description: Performs quality and adapter trimming on paired end and single end reads
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keywords:
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- trimming
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- adapter trimming
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- quality trimming
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tools:
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- "trimmomatic":
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description: "A flexible read trimming tool for Illumina NGS data"
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homepage: "http://www.usadellab.org/cms/?page=trimmomatic"
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documentation: "https://github.com/usadellab/Trimmomatic"
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tool_dev_url: "None"
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doi: "10.1093/bioinformatics/btu170"
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licence: "['GPL v3']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- reads:
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type: file
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description: |
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Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively.
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pattern: "*.fastq.gz"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- trimmed_reads:
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type: file
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description: The trimmed/modified paired end fastq reads
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pattern: "*.paired.trim*.fastq.gz"
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- unpaired_reads:
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type: file
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description: The trimmed/modified unpaired end fastq reads
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pattern: "*.unpaired.trim_*.fastq.gz"
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- log:
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type: file
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description: trimmomatic log file
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pattern: "*.log"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@alyssa-ab"
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