name: bowtie2_align description: Align reads to a reference genome using bowtie2 keywords: - align - fasta - genome - reference tools: - bowtie2: description: | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml doi: 10.1038/nmeth.1923 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: Bowtie2 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" - log: type: file description: Aligment log pattern: "*.log" authors: - "@joseespinosa" - "@drpatelh"