Description

Concatenates fastq files. Supports both compressed (.gz) and uncompressed inputs; uncompressed files are automatically gzip-compressed during concatenation.

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 to be concatenated. Accepts both gzip-compressed (.fastq.gz) and uncompressed (.fastq) files.

Output

name:type
description
pattern

reads{:bash}

meta{:bash}

:map

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

*.merged.fastq.gz{:bash}

:file

Merged fastq file

*.{merged.fastq.gz}

versions_cat{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

cat{:bash}

:string

The tool name

cat --version 2>&1 | head -n 1 | sed 's/^.*coreutils) //; s/ .*\$//'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

cat{:bash}

:string

The tool name

cat --version 2>&1 | head -n 1 | sed 's/^.*coreutils) //; s/ .*\$//'{:bash}

:eval

The expression to obtain the version of the tool

Tools

cat
GPL-3.0-or-later

The cat utility reads files sequentially, writing them to the standard output.

gnu.org/software/coreutils/manual/html_node/cat-invocation
included in
airrflowbacassbamtofastqcircdnacircrnacrisprseqcutandrundenovotranscriptgenomeannotatorhlatypinglncpipemagmagmapmetatdenovomethylseqnascentpixelatorriboseqrnadnavarrnafusionrnaseqrnasplicernavarsammyseqsarekscnanoseqsmrnaseqtaxprofilerviralmetagenomeviralrecon
maintainers
Github user joseespinosa
Github user drpatelh
get in touch
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