Description

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

Input

Name
Description
Pattern

meta (map)

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

files_in (file)

List of either compressed or uncompressed files

*

sort (boolean)

Sort concatenated BED output by chrom/start if true

Output

Name
Description
Pattern

file_out

meta (map)

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

${prefix} (file)

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

${file_out}

versions_find

${task.process} (string)

The name of the process

find (string)

The name of the tool

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

The expression to obtain the version of the tool

versions_pigz

${task.process} (string)

The name of the process

pigz (string)

The name of the tool

pigz --version 2>&1 | sed 's/pigz //g' (eval)

The expression to obtain the version of the tool

versions_coreutils

${task.process} (string)

The name of the process

coreutils (string)

The name of the tool

cat --version | sed '1!d; s/.* //' (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

find (string)

The name of the tool

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

The expression to obtain the version of the tool

${task.process} (string)

The name of the process

pigz (string)

The name of the tool

pigz --version 2>&1 | sed 's/pigz //g' (eval)

The expression to obtain the version of the tool

${task.process} (string)

The name of the process

coreutils (string)

The name of the tool

cat --version | sed '1!d; s/.* //' (eval)

The expression to obtain the version of the tool

Tools

find Documentation

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

License: GPL-3.0-or-later

pigz Documentation

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.

License: other
Authors