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

]

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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

output (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
included in
funcscan
author
Github user jfy133
get in touch
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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