name: bwa mem description: Performs fastq alignment to a fasta reference using the burrows-wheeler aligner keywords: - mem - bwa - alignment tools: - bwa: description: | BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. homepage: http://bio-bwa.sourceforge.net/ documentation: http://www.htslib.org/doc/samtools.html arxiv: arXiv:1303.3997 input: - - id: type: val description: read/read pair id - reads: type: file description: Input fastq file pattern: *.{fastq,fq} - index: type: file description: bwa indexes file pattern: *.{amb,ann,bwt,pac,sa} - prefix: type: val description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified. output: - - bam: type: file description: Output bam file pattern: *.bam - bamindex: type: file description: Output bam index file pattern: *.bai authors: - @jeremy1805