modules/fastqc

Run FastQC on sequenced reads

quality controlqcadaptersfastq

https://github.com/nf-core/modules/[...]/modules/nf-core/fastqc

Description

Run FastQC on sequenced reads

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`reads`
`:file`

List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

Output

name:type

description

pattern

`html`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.html`
`:file`

FastQC report

*_{fastqc.html}

`zip`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.zip`
`:file`

FastQC report archive

*_{fastqc.zip}

`versions_fastqc`

`${task.process}`
`:string`

The process the versions were collected from

`fastqc`
`:string`

The tool name

`fastqc --version | sed "/FastQC v/!d; s/.*v//`
`:string`

The command used to generate the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`fastqc`
`:string`

The tool name

`fastqc --version | sed "/FastQC v/!d; s/.*v//`
`:string`

The command used to generate the version of the tool

Tools

fastqc
GPL-2.0-only

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.

bioinformatics.babraham.ac.uk/projects/fastqc bioinformatics.babraham.ac.uk/projects/fastqc/Help

modules/fastqc

Description

Input

`meta`
`:map`

`reads`
`:file`

Output

`html`

`meta`
`:map`

`*.html`
`:file`

`zip`

`meta`
`:map`

`*.zip`
`:file`

`versions_fastqc`

`${task.process}`
`:string`

`fastqc`
`:string`

`fastqc --version | sed "/FastQC v/!d; s/.*v//`
`:string`

Topics

`versions`

`${task.process}`
`:string`

`fastqc`
`:string`

`fastqc --version | sed "/FastQC v/!d; s/.*v//`
`:string`

Tools

fastqc
GPL-2.0-only

included in

maintainers

get in touch

modules/fastqc

Description

Input

meta:map

reads:file

Output

html

meta:map

*.html:file

zip

meta:map

*.zip:file

versions_fastqc

${task.process}:string

fastqc:string

fastqc --version | sed "/FastQC v/!d; s/.*v//:string

Topics

versions

${task.process}:string

fastqc:string

fastqc --version | sed "/FastQC v/!d; s/.*v//:string

Tools

fastqc GPL-2.0-only

included in

maintainers

get in touch

`meta`
`:map`

`reads`
`:file`

`html`

`meta`
`:map`

`*.html`
`:file`

`zip`

`meta`
`:map`

`*.zip`
`:file`

`versions_fastqc`

`${task.process}`
`:string`

`fastqc`
`:string`

`fastqc --version | sed "/FastQC v/!d; s/.*v//`
`:string`

`versions`

`${task.process}`
`:string`

`fastqc`
`:string`

`fastqc --version | sed "/FastQC v/!d; s/.*v//`
`:string`

fastqc
GPL-2.0-only