modules/find_unpigz

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

gzipfindpigz

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

Description

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

Input

name:type

description

pattern

`meta`
`:map`

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

`files_in`
`:file`

List of gzipped files to decompress

*.gz

Output

name:type

description

pattern

`file_out`

`meta`
`:map`

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

*

`ungzipped/*`
`:file`

Files that have been decompressed

*

`versions_find`

`${task.process}`
`:string`

The process the versions were collected from

`find`
`:string`

The tool name

`find --version | sed '1!d; s/.* //'`
`:eval`

The expression to obtain the version of the tool

`versions_pigz`

`${task.process}`
`:string`

The process the versions were collected from

`pigz`
`:string`

The tool name

`pigz --version 2>&1 | sed "s/^.pigz[[:space:]]//"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`find`
`:string`

The tool name

`find --version | sed '1!d; s/.* //'`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The process the versions were collected from

`pigz`
`:string`

The tool name

`pigz --version 2>&1 | sed "s/^.pigz[[:space:]]//"`
`: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

modules/find_unpigz

Description

Input

`meta`
`:map`

`files_in`
`:file`

Output

`file_out`

`meta`
`:map`

`ungzipped/*`
`:file`

`versions_find`

`${task.process}`
`:string`

`find`
`:string`

`find --version | sed '1!d; s/.* //'`
`:eval`

`versions_pigz`

`${task.process}`
`:string`

`pigz`
`:string`

`pigz --version 2>&1 | sed "s/^.pigz[[:space:]]//"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`find`
`:string`

`find --version | sed '1!d; s/.* //'`
`:eval`

`${task.process}`
`:string`

`pigz`
`:string`

`pigz --version 2>&1 | sed "s/^.pigz[[:space:]]//"`
`:eval`

Tools

find
GPL-3.0-or-later

pigz
other

included in

maintainer

get in touch

modules/find_unpigz

Description

Input

meta:map

files_in:file

Output

file_out

meta:map

ungzipped/*:file

versions_find

${task.process}:string

find:string

find --version | sed '1!d; s/.* //':eval

versions_pigz

${task.process}:string

pigz:string

pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//":eval

Topics

versions

${task.process}:string

find:string

find --version | sed '1!d; s/.* //':eval

${task.process}:string

pigz:string

pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//":eval

Tools

find GPL-3.0-or-later

pigz other

included in

maintainer

get in touch

`meta`
`:map`

`files_in`
`:file`

`file_out`

`meta`
`:map`

`ungzipped/*`
`:file`

`versions_find`

`${task.process}`
`:string`

`find`
`:string`

`find --version | sed '1!d; s/.* //'`
`:eval`

`versions_pigz`

`${task.process}`
`:string`

`pigz`
`:string`

`pigz --version 2>&1 | sed "s/^.pigz[[:space:]]//"`
`:eval`

`versions`

`${task.process}`
`:string`

`find`
`:string`

`find --version | sed '1!d; s/.* //'`
`:eval`

`${task.process}`
`:string`

`pigz`
`:string`

`pigz --version 2>&1 | sed "s/^.pigz[[:space:]]//"`
`:eval`

find
GPL-3.0-or-later

pigz
other