name: bwa_mem description: Performs fastq alignment to a fasta reference using BWA keywords: - mem - bwa - alignment - map - fastq - bam - sam 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 licence: ["GPL-3.0-or-later"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - index: type: file description: BWA genome index files pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - sort_bam: type: boolean description: use samtools sort (true) or samtools view (false) pattern: "true or false" output: - bam: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@drpatelh" - "@jeremy1805"