Description

fq subsample outputs a subset of records from single or paired FASTQ files. This requires a seed (—seed) to be set in ext.args.

Input

name:type
description
pattern

meta

:map

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

fastq

:file

FASTQ file

*.{fq,fastq}{,.gz}

Output

name:type
description
pattern

fastq

meta

:map

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

*.fastq.gz

:file

Randomly sampled FASTQ files.

*_R[12].fastq.gz

versions_fq

${task.process}

:string

The name of the process

fq

:string

The name of the tool

fq subsample --version | sed 's/fq-subsample //; s/ .*//'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

fq

:string

The name of the tool

fq subsample --version | sed 's/fq-subsample //; s/ .*//'

:eval

The expression to obtain the version of the tool

Tools

fq
MIT

fq is a library to generate and validate FASTQ file pairs.

github.com/stjude-rust-labs/fq
included in
lncpiperiboseqrnaseq
maintainer
Github user adamrtalbot
get in touch
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