name: bwa_sampe description: Convert paired-end bwa SA coordinate files to SAM format keywords: - bwa - aln - short-read - align - reference - fasta - map - sam - bam 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: FASTQ files specified alongside meta in input channel. pattern: "*.{fastq,fq}.gz" - sai: type: file description: SAI file specified alongside meta and reads in input channel. pattern: "*.sai" - index: type: directory description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX pattern: "bwa/" 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}" - bam: type: file description: BAM file pattern: "*.bam" authors: - "@jfy133"