bwa_mem

Performs fastq alignment to a fasta reference using BWA. Adapted from the nf-core bwa-mem module.

nf-core modules \
  --git-remote https://github.com/CCBR/nf-modules \
  install bwa/mem

https://github.com/CCBR/nf-modules/…/modules/CCBR/bwa/mem/

Input

name	type	description	pattern
meta	map	Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]	NA
reads	file	List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.	NA
index	file	BWA genome index files	Directory containing BWA index *.{amb,ann,bwt,pac,sa}

Output

name	type	description	pattern
bam	file	Output BAM file containing read alignments	*.{bam}
bai	file	Output BAI index file	*.{bai}
versions	file	File containing software versions	versions.yml

Tools

bwa

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BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.