2020-08-06 23:50:49 +00:00
|
|
|
name: fastqc
|
2019-12-05 14:18:09 +00:00
|
|
|
description: Run FastQC on sequenced reads
|
|
|
|
|
keywords:
|
2020-08-07 14:05:25 +00:00
|
|
|
- quality control
|
|
|
|
|
- qc
|
|
|
|
|
- adapters
|
|
|
|
|
- fastq
|
2019-12-05 14:18:09 +00:00
|
|
|
tools:
|
2020-08-07 14:05:25 +00:00
|
|
|
- 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/
|
2019-12-05 14:18:09 +00:00
|
|
|
input:
|
2020-08-07 14:05:25 +00:00
|
|
|
- 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.
|
2019-12-05 14:18:09 +00:00
|
|
|
output:
|
2020-08-07 14:05:25 +00:00
|
|
|
- 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}"
|
2019-12-05 14:18:09 +00:00
|
|
|
authors:
|
2020-08-07 14:05:25 +00:00
|
|
|
- "@drpatelh"
|
|
|
|
|
- "@grst"
|
|
|
|
|
- "@ewels"
|
|
|
|
|
- "@FelixKrueger"
|
