Description

A module for decompressing a large number of gzipped files, getting around the UNIX terminal argument limit

Input

name:type
description
pattern

meta{:bash}

:map

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

files_in{:bash}

:file

List of gzipped files to decompress

*.gz

Output

name:type
description
pattern

file_out{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*

ungzipped/*{:bash}

:file

Files that have been decompressed

*

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
createtaxdb
maintainer
Github user Biowilko
get in touch
Ask a question on Slack Open an issue on GitHub