fastq_preprocess_seqkit

Subworkflow that preprocesses FASTQ files

fastqseqkitpreprocessing

Description

Subworkflow that preprocesses FASTQ files

name

description

pattern

Channel containing sample metadata and FASTQ files.
Structure: [ val(meta), [ fastq ] ]
Where meta is a map containing at least:

id: sample identifier
single_end: boolean indicating if data is single-end (true) or paired-end (false)

*.{fastq,fastq.gz,fq,fq.gz}

If true, skips the seqkit_sana_pair subworkflow.

If true, skips the seqkit_seq process.

If true, skips the seqkit_replace process.

If true, skips the seqkit_rmdup process.

name

description

pattern

Channel containing filtered FASTQ files.
Structure: [ val(meta), [ fastq ] ]

*.{fastq,fastq.gz,fq,fq.gz}

File containing software versions
Structure: [ path(versions.yml) ]

versions.yml