mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
59 lines
1.7 KiB
YAML
59 lines
1.7 KiB
YAML
name: trimgalore
|
|
description: Trim FastQ files using Trim Galore!
|
|
keywords:
|
|
- trimming
|
|
- adapters
|
|
- sequencing adapters
|
|
- fastq
|
|
tools:
|
|
- trimgalore:
|
|
description: |
|
|
A wrapper tool around Cutadapt and FastQC to consistently apply quality
|
|
and adapter trimming to FastQ files, with some extra functionality for
|
|
MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
|
|
homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
|
|
documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md
|
|
licence: ["GPL-3.0-or-later"]
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- reads:
|
|
type: file
|
|
description: |
|
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
|
respectively.
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- reads:
|
|
type: file
|
|
description: |
|
|
List of input adapter trimmed FastQ files of size 1 and 2 for
|
|
single-end and paired-end data, respectively.
|
|
pattern: "*.{fq.gz}"
|
|
- html:
|
|
type: file
|
|
description: FastQC report (optional)
|
|
pattern: "*_{fastqc.html}"
|
|
- zip:
|
|
type: file
|
|
description: FastQC report archive (optional)
|
|
pattern: "*_{fastqc.zip}"
|
|
- log:
|
|
type: file
|
|
description: Trim Galore! trimming report
|
|
pattern: "*_{report.txt}"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
authors:
|
|
- "@drpatelh"
|
|
- "@ewels"
|
|
- "@FelixKrueger"
|