Description

Run FastQC on sequenced reads

Input

name:type
description
pattern

meta{:bash}

:map

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

reads{:bash}

: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{:bash}

meta{:bash}

:map

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

*.html{:bash}

:file

FastQC report

*_{fastqc.html}

zip{:bash}

meta{:bash}

:map

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

*.zip{:bash}

:file

FastQC report archive

*_{fastqc.zip}

versions_fastqc{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

fastqc{:bash}

:string

The tool name

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

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

fastqc{:bash}

:string

The tool name

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

: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
included in
abotyperairrflowalleleexpressionampliseqatacseqbacassbamtofastqcallingcardschipseqcircdnacircrnacoproidcrisprseqcutandrundeepmutscandemodemultiplexdenovotranscriptdetaxizerevexplorerfastqrepairfastquorumgenomeannotatorgenomeassemblergenomeqcgenomeskimhgtseqhichicarhlatypingliverctanalysislncpipemagmagmapmarsseqmetaboignitermetatdenovomethylarraymethylongmethylseqmitodetectmultiplesequencealignnanoseqnascentomicsgenetraitassociationpacvarpanoramaseqpathogensurveillancephageannotatorradseqrarediseasereadsimulatorriboseqrnadnavarrnafusionrnaseqrnasplicernavarsammyseqsarekscnanoseqscrnaseqseqinspectorsmrnaseqspatialvissdstaxprofilertbanalyzertroughgraphvariantcatalogueviralintegrationviralmetagenomeviralrecon
maintainers
Github user drpatelh
Github user grst
Github user ewels
Github user FelixKrueger
get in touch
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