name: bowtie_align description: Align reads to a reference genome using bowtie keywords: - align - fasta - genome - reference tools: - bowtie: description: | bowtie is a software package for mapping DNA sequences against a large reference genome, such as the human genome. homepage: http://bowtie-bio.sourceforge.net/index.shtml documentation: http://bowtie-bio.sourceforge.net/manual.shtml arxiv: arXiv:1303.3997 licence: ['Artistic-2.0'] 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: Bowtie genome index files pattern: "*.ebwt" output: - bam: type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - versions: type: file description: File containing software versions pattern: "versions.yml" - fastq: type: file description: Unaligned FastQ files pattern: "*.fastq.gz" authors: - "@kevinmenden"