reads_bwamem2_decontamination

Description¶

Short-reads mapping to a reference genome and remove matching reads

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install reads_bwamem2_decontamination

Keywords: decontamination, short-reads, mapping

This subworkflow uses the following components:

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	-
`reads`	file	A list of input FastQ files of size 1 or 2 for single-end and paired-end data, respectively	`*.{fastq/fq}.gz`
`meta2`	map	Groovy Map containing reference genome information e.g. [ id:'ref_name' ]	-
`ref_index`	file	A list of BWA index reference files	`*.{amb,ann,bwt,pac,sa}`

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	-
`decont_reads`	file	A list of decontaminated FastQ files of size 1 or 2 for single-end and paired-end data, respectively	-
`versions`	file	File containing software versions	`versions.yml`

Maintainers