Description

Use seqkit to find/replace strings within sequences and sequence headers

Input

name:type
description
pattern

meta:map

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

]

fastx:file

fasta/q file

*.{fasta,fastq,fa,fq,fas,fna,faa}*

Output

name:type
description
pattern

fastx

meta:map

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

]

*.fast*:file

fasta/q file with replaced values

*.{fasta,fastq,fa,fq,fas,fna,faa}*

versions

versions.yml:file

File containing software versions

versions.yml

Tools

seqkit

Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.