picard_samtofastq

Converts a BAM or SAM file to fastq. Adapted from the nf-core gatk4 samtofastq module.

nf-core modules \
  --git-remote https://github.com/CCBR/nf-modules \
  install picard/samtofastq

https://github.com/CCBR/nf-modules/…/modules/CCBR/picard/samtofastq/

Input

name	type	description
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
bam	file	SAM or BAM file

Output

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
versions	file	File containing software versions	versions.yml
fastq	file	fastq files	*.{fastq}

Tools

picard

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A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.