mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
67 lines
2.1 KiB
YAML
67 lines
2.1 KiB
YAML
name: fastqc
|
|
description: Run FastQC on sequenced reads
|
|
keywords:
|
|
- quality control
|
|
- qc
|
|
- adapters
|
|
- fastq
|
|
tools:
|
|
- fastqc:
|
|
description: |
|
|
FastQC gives general quality metrics about your reads.
|
|
It provides information about the quality score distribution
|
|
across your reads, the per base sequence content (%A/C/G/T).
|
|
You get information about adapter contamination and other
|
|
overrepresented sequences.
|
|
homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
|
|
documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
|
|
params:
|
|
- outdir:
|
|
type: string
|
|
description: |
|
|
The pipeline's output directory. By default, the module will
|
|
output files into `$params.outdir/<SOFTWARE>`
|
|
- publish_dir_mode:
|
|
type: string
|
|
description: |
|
|
Value for the Nextflow `publishDir` mode parameter.
|
|
Available: symlink, rellink, link, copy, copyNoFollow, move.
|
|
- enable_conda:
|
|
type: boolean
|
|
description: |
|
|
Run the module with Conda using the software specified
|
|
via the `conda` directive
|
|
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 ]
|
|
- html:
|
|
type: file
|
|
description: FastQC report
|
|
pattern: "*_{fastqc.html}"
|
|
- zip:
|
|
type: file
|
|
description: FastQC report archive
|
|
pattern: "*_{fastqc.zip}"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
authors:
|
|
- "@drpatelh"
|
|
- "@grst"
|
|
- "@ewels"
|
|
- "@FelixKrueger"
|