Description

Transforms sequences (extract ID, filter by length, remove gaps, reverse complement…)

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

fastx{:bash}

:file

Input fasta/fastq file

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

Output

name:type
description
pattern

fastx{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

${prefix}.${extension}{:bash}

:file

Output fasta/fastq file

*.{fasta,fasta.gz,fastq,fastq.gz}

log{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1' ]

*.log{:bash}

:file

Log containing information regarding removed duplicates

*.log

versions_seqkit{:bash}

${task.process}{:bash}

:string

The name of the process

seqkit{:bash}

:string

The name of the tool

seqkit version | sed 's/^.*v//'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

seqkit{:bash}

:string

The name of the tool

seqkit version | sed 's/^.*v//'{:bash}

:eval

The expression to obtain the version of the tool

Tools

included in
proteinannotatorproteinfamilies
maintainer
Github user GallVp
get in touch
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