mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
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"
|
|
description: Performs quality and adapter trimming on paired end and single end reads
|
|
keywords:
|
|
- trimming
|
|
- adapter trimming
|
|
- quality trimming
|
|
|
|
tools:
|
|
- "trimmomatic":
|
|
description: "A flexible read trimming tool for Illumina NGS data"
|
|
homepage: "http://www.usadellab.org/cms/?page=trimmomatic"
|
|
documentation: "https://github.com/usadellab/Trimmomatic"
|
|
tool_dev_url: "None"
|
|
doi: "10.1093/bioinformatics/btu170"
|
|
licence: "['GPL v3']"
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- reads:
|
|
type: file
|
|
description: |
|
|
Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively.
|
|
pattern: "*.fastq.gz"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- trimmed_reads:
|
|
type: file
|
|
description: The trimmed/modified paired end fastq reads
|
|
pattern: "*.paired.trim*.fastq.gz"
|
|
- unpaired_reads:
|
|
type: file
|
|
description: The trimmed/modified unpaired end fastq reads
|
|
pattern: "*.unpaired.trim_*.fastq.gz"
|
|
- log:
|
|
type: file
|
|
description: trimmomatic log file
|
|
pattern: "*.log"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
|
|
authors:
|
|
- "@alyssa-ab"
|