faa_seqfu_seqkit

Subworkflow that optionally preprocesses amino acid FASTA sequences (seqkit seq/replace/rmdup), computes sequence statistics before and after preprocessing using seqfu stats, and exports MultiQC-compatible statistics and software versions.

fastaproteinpreprocessingstatisticsquality check

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/faa_seqfu_seqkit

Description

Input

name

description

pattern

`ch_fasta`

Amino acid sequences fasta file.
Structure: [ val(meta), [ path(fasta) ] ]

`skip_preprocessing`

If true, skip seqkit-based preprocessing steps and only compute
initial sequence statistics.

Output

name

description

pattern

`fasta`

Contains the final amino acid FASTA file
(either preprocessed or original if preprocessing is skipped).

`multiqc_files`

Statistics file for MultiQC.

`versions`

Versions file containing the software versions used in the workflow.

faa_seqfu_seqkit

Description

Input

`ch_fasta`

`skip_preprocessing`

Output

`fasta`

`multiqc_files`

`versions`

included in

included modules and subworkflows

maintainer

get in touch