samtools_bam2fq

Description¶

The module uses bam2fq method from samtools to convert a SAM, BAM or CRAM file to FASTQ format

Keywords: bam2fq, samtools, fastq

nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install samtools/bam2fq

Tools for dealing with SAM, BAM and CRAM files

Name	Type	Description	Pattern
`meta`	map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]	-
`bam_file`	file	Sorted BAM file	-
`split`	boolean	True or false indicating whether the output is for single or paired-end reads	-

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

Maintainers