Description

A module for concatenation of gzipped or uncompressed files getting around UNIX terminal argument size

Input

name:type
description
pattern

meta{:bash}

:map

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

files_in{:bash}

:file

List of either compressed or uncompressed files

*

Output

name:type
description
pattern

file_out{:bash}

meta{:bash}

:map

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

${prefix}{:bash}

:file

Concatenated file. Will be gzipped if ${prefix} ends with “.gz” or inputs are gzipped, will be uncompressed otherwise.

${file_out}

versions_find{:bash}

${task.process}{:bash}

:string

The name of the process

find{:bash}

:string

The name of the tool

find --version | sed '1!d; s/.* //'{:bash}

:eval

The expression to obtain the version of the tool

versions_pigz{:bash}

${task.process}{:bash}

:string

The name of the process

pigz{:bash}

:string

The name of the tool

pigz --version 2>&1 | sed 's/pigz //g'{:bash}

:eval

The expression to obtain the version of the tool

versions_coreutils{:bash}

${task.process}{:bash}

:string

The name of the process

coreutils{:bash}

:string

The name of the tool

cat --version | sed '1!d; s/.* //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

find{:bash}

:string

The name of the tool

find --version | sed '1!d; s/.* //'{:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

pigz{:bash}

:string

The name of the tool

pigz --version 2>&1 | sed 's/pigz //g'{:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

coreutils{:bash}

:string

The name of the tool

cat --version | sed '1!d; s/.* //'{:bash}

:eval

The expression to obtain the version of the tool

Tools

find
GPL-3.0-or-later

GNU find searches the directory tree rooted at each given starting-point by evaluating the given expression

man7.org/linux/man-pages/man1/find.1

pigz
other

pigz, which stands for Parallel Implementation of GZip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.

zlib.net/pigz/pigz.pdf
included in
createtaxdbproteinfamilies
maintainer
Github user BioWilko
get in touch
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