fastq_index_filter_deacon

Decontaminate FastQ files by filtering reads that match a reference genome using Deacon

filterindexfastafastqgenomereferenceminimizerdecontamination

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

Description

Decontaminate FastQ files by filtering reads that match a reference genome using Deacon

Input

name

description

pattern

`ch_fasta_reads`

Input genome fasta file and a list of FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
Structure: [ val(meta), path(fasta), [ path(reads) ] ]

Output

name

description

pattern

`index`

Deacon minimizer index file
Structure: [ val(meta), path(index) ]

.idx

`fastq_filtered`

List of output filtered FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
Structure: [ val(meta), path(${prefix}*.fq) ]

*.fq.gz

`summary`

JSON file containing summary of results.
Structure: [ val(meta), path(${prefix}.json) ]

*.json

`versions`

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

versions.yml