fastq_sanitise_seqkit

Filters and reports malformed FASTQ sequences with seqkit/sana, and then pairs any paired-end files using seqkit/pair

fastqquality controlfilteringmalformedpairingseqkitpreprocessing

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

Description

Filters and reports malformed FASTQ sequences with seqkit/sana, and then pairs any paired-end files using seqkit/pair

Input

name

description

pattern

`ch_reads`

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}

Output

name

description

pattern

`reads`

Channel containing filtered (i.e., non-malformed) and paired FASTQ files.
For single-end data: returns filtered reads
For paired-end data: returns properly paired reads and any unpaired reads
Structure: [ val(meta), [ fastq ] ]

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

`versions`

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

versions.yml