name: bwa_aln description: Find SA coordinates of the input reads for bwa short-read mapping keywords: - bwa - aln - short-read - align - reference - fasta - map - fastq 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://bio-bwa.sourceforge.net/ doi: "10.1093/bioinformatics/btp324" licence: ['GPL v3'] 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}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - version: type: file description: File containing software version pattern: "*.{version.txt}" - sai: type: file description: Single or paired SA coordinate files pattern: "*.sai" authors: - "@jfy133"