Description

Bioawk is an extension to Brian Kernighan’s awk, adding the support of several common biological data formats.

Input

name:type
description
pattern

meta:map

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

input:file

Input sequence biological sequence file (optionally gzipped) to be manipulated via program specified in $args.

*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}

Output

name:type
description
pattern

output

meta:map

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

*.gz:file

Manipulated and gzipped version of input sequence file following program specified in args. File name will be what is specified in $prefix. Do not include .gz suffix in $prefix! Output files` will be gzipped for you!

*.gz

versions

versions.yml:file

File containing software versions

versions.yml

Tools

bioawk
Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1)

BWK awk modified for biological data

github.com/lh3/bioawk
included in
circrnarnafusionsmrnaseq
maintainer
Github user jfy133
get in touch
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