modules/find_concatenate

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

concatenategzipcatfindpigz

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

Description

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

Input

name:type

description

pattern

`meta:map`

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

`files_in:file`

List of either compressed or uncompressed files

*

Output

name:type

description

pattern

`file_out`

`meta:map`

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

`${prefix}:file`

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

${file_out}

`versions`

`versions.yml: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.

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

modules/find_concatenate

Description

Input

`meta:map`

`files_in:file`

Output

`file_out`

`meta:map`

`${prefix}:file`

`versions`

`versions.yml:file`

Tools

find
GPL-3.0-or-later

pigz
other

included in

maintainer

get in touch

modules/find_concatenate

Description

Input

meta:map

files_in:file

Output

file_out

meta:map

${prefix}:file

versions

versions.yml:file

Tools

find GPL-3.0-or-later

pigz other

included in

maintainer

get in touch

`meta:map`

`files_in:file`

`file_out`

`meta:map`

`${prefix}:file`

`versions`

`versions.yml:file`

find
GPL-3.0-or-later

pigz
other