Description

Common transformation operations on FASTA or FASTQ files.

Input

name:type
description
pattern

meta

:map

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

fastx

:file

A FASTQ or FASTA file

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

Output

name:type
description
pattern

fastx

meta

:map

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

*.gz

:file

FASTQ/FASTA file containing renamed sequences

*.{fastq.gz, fasta.gz}

versions_seqtk

${task.process}

:string

The name of the process

seqtk

:string

The name of the tool

seqtk 2>&1 | sed -n 's/^Version: //p'

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

seqtk

:string

The name of the tool

seqtk 2>&1 | sed -n 's/^Version: //p'

:eval

The expression to obtain the version of the tool

Tools

seqtk
MIT

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk seq command enables common transformation operations on FASTA or FASTQ files.

github.com/lh3/seqtk docs.csc.fi/apps/seqtk https://github.com/lh3/seqtk
included in
crisprseqmetatdenovoradseq
maintainers
Github user hseabolt
Github user mjcipriano
Github user sateeshperi
get in touch
Ask a question on Slack Open an issue on GitHub