modules/trimgalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

trimmingadapterssequencingfastq

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

Description

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

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

`reads`

`meta`
`:map`

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

`*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz`
`:file`

The trimmed/modified fastq reads

*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz

`log`

`meta`
`:map`

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

`*report.txt`
`:file`

trimgalore log file

*report.txt

`unpaired`

`meta`
`:map`

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

`*unpaired{,_1,_2}.fq.gz`
`:file`

unpaired reads when —retain_unpaired flag is used

*unpaired*.fq.gz

`html`

`meta`
`:map`

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

`*.html`
`:file`

FastQC HTML report after trimming when the —fastqc flag is used

*_fastqc.html

`zip`

`meta`
`:map`

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

`*.zip`
`:file`

FastQC report output zip after trimming when the —fastqc flag is used

*_fastqc.zip

`versions_trimgalore`

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

The name of the process

`trimgalore`
`:string`

The name of the tool

`trim_galore --version | grep -Eo "[0-9]+(\.[0-9]+)+"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`trimgalore`
`:string`

The name of the tool

`trim_galore --version | grep -Eo "[0-9]+(\.[0-9]+)+"`
`:eval`

The expression to obtain the version of the tool

Tools

trimgalore
GPL-3.0-or-later

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.

bioinformatics.babraham.ac.uk/projects/trim_galore github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md

modules/trimgalore

Description

Input

`meta`
`:map`

`reads`
`:file`

Output

`reads`

`meta`
`:map`

`*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz`
`:file`

`log`

`meta`
`:map`

`*report.txt`
`:file`

`unpaired`

`meta`
`:map`

`*unpaired{,_1,_2}.fq.gz`
`:file`

`html`

`meta`
`:map`

`*.html`
`:file`

`zip`

`meta`
`:map`

`*.zip`
`:file`

`versions_trimgalore`

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

`trimgalore`
`:string`

`trim_galore --version | grep -Eo "[0-9]+(\.[0-9]+)+"`
`:eval`

Topics

`versions`

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

`trimgalore`
`:string`

`trim_galore --version | grep -Eo "[0-9]+(\.[0-9]+)+"`
`:eval`

Tools

trimgalore
GPL-3.0-or-later

included in

maintainers

get in touch

modules/trimgalore

Description

Input

meta:map

reads:file

Output

reads

meta:map

*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz:file

log

meta:map

*report.txt:file

unpaired

meta:map

*unpaired{,_1,_2}.fq.gz:file

html

meta:map

*.html:file

zip

meta:map

*.zip:file

versions_trimgalore

${task.process}:string

trimgalore:string

trim_galore --version | grep -Eo "[0-9]+(\.[0-9]+)+":eval

Topics

versions

${task.process}:string

trimgalore:string

trim_galore --version | grep -Eo "[0-9]+(\.[0-9]+)+":eval

Tools

trimgalore GPL-3.0-or-later

included in

maintainers

get in touch

`meta`
`:map`

`reads`
`:file`

`reads`

`meta`
`:map`

`*{3prime,5prime,trimmed,val}{,_1,_2}.fq.gz`
`:file`

`log`

`meta`
`:map`

`*report.txt`
`:file`

`unpaired`

`meta`
`:map`

`*unpaired{,_1,_2}.fq.gz`
`:file`

`html`

`meta`
`:map`

`*.html`
`:file`

`zip`

`meta`
`:map`

`*.zip`
`:file`

`versions_trimgalore`

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

`trimgalore`
`:string`

`trim_galore --version | grep -Eo "[0-9]+(\.[0-9]+)+"`
`:eval`

`versions`

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

`trimgalore`
`:string`

`trim_galore --version | grep -Eo "[0-9]+(\.[0-9]+)+"`
`:eval`

trimgalore
GPL-3.0-or-later