custom_bam2fastq

The module converts a BAM file to FASTQ format. It uses samtools bam2fq if reads are single end, or picard SamToFastq if reads are paired.

nf-core modules \
  --git-remote https://github.com/CCBR/nf-modules \
  install custom/bam2fastq

https://github.com/CCBR/nf-modules/…/modules/CCBR/custom/bam2fastq/

Input

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
bam	file	BAM file	*.{bam,cram,sam}
bai	file	BAI (bam index) file	*.{bai}

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
reads	file	1 fastq file if single end, or 2 fastq files if paired-end.	*.fastq.gz
unpaired	file	unpaired reads	*.fastq.gz

Tools

samtools

  Docs     MIT

Tools for dealing with SAM, BAM and CRAM files

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.