modules/seqkit_fx2tab

Convert FASTA/Q to tabular format, and provide various information, like sequence length, GC content/GC skew.

fastafastqtexttabularconvert

https://github.com/nf-core/modules/[...]/modules/nf-core/seqkit/fx2tab

Description

Convert FASTA/Q to tabular format, and provide various information, like sequence length, GC content/GC skew.

Input

name:type

description

pattern

`meta:map`

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

]

`fastx:file`

Sequence file in fasta/q format

*.{fasta,fastq,fa,fq,fas,fna,faa}[.gz,.zst]

Output

name:type

description

pattern

`text`

`meta:map`

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

]

`.txt:file`

Text file in tabular format

*.txt[.gz,.zstd,.zst]

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

seqkit
MIT

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

github.com/shenwei356/seqkit bioinf.shenwei.me/seqkit 10.1371/journal.pone.0163962

modules/seqkit_fx2tab

Description

Input

meta:map

fastx:file

Output

text

meta:map

*.txt*:file

versions

versions.yml:file

Tools

seqkit MIT

`meta:map`

`fastx:file`

`text`

`meta:map`

`.txt:file`

`versions`

`versions.yml:file`

seqkit
MIT