bwamem2decontnobams

Description¶

Decontamination module using bwamem2 and samtools that generates fastq files on the fly

Keywords: alignment, decontamination, fastq

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install bwamem2decontnobams

Mapping DNA sequences against a large reference genome

Tools for dealing with SAM, BAM and CRAM files

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`	-
`reads`	file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively	-
`meta2`	map	Groovy Map containing reference genome information e.g. [ id:'ref_name' ]	-
`index`	file	A list of BWA index files	-

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`	-
`versions`	file	File containing software versions	`versions.yml`
`decont_reads`	file	List of fastq files. Two files for paired-end reads and one file for single-end reads	-

Maintainers