Description

If you are like many computer users, you would frequently like to make changes in various text files wherever certain patterns appear, or extract data from parts of certain lines while discarding the rest. The job is easy with awk, especially the GNU implementation gawk.

Input

name:type
description
pattern

meta:map

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

input:file

The input file - Specify the logic that needs to be executed on this file on the ext.args2 or in the program file. If the files have a .gz extension, they will be unzipped using zcat.

*

program_file:file

Optional file containing logic for awk to execute. If you don’t wish to use a file, you can use ext.args2 to specify the logic.

*

disable_redirect_output:boolean

Disable the redirection of awk output to a given file. This is useful if you want to use awk’s built-in redirect to write files instead of the shell’s redirect.

Output

name:type
description
pattern

output

meta:map

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

*.${suffix}:file

The output file - if using shell redirection, specify the name of this file using ext.prefix and the extension using ext.suffix. Otherwise, ensure the awk program produces files with the extension in ext.suffix.

*

versions

versions.yml:file

File containing software versions

versions.yml

Tools

circrna deepmodeloptim denovotranscript phaseimpute references sarek smrnaseq tfactivity
Github user nvnieuwk
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