name: bbmap_align description: write your description here keywords: - align - map - fasta - genome - reference tools: - bbmap: description: BBMap is a short read aligner, as well as various other bioinformatic tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ tool_dev_url: None doi: "" licence: ['UC-LBL license (see package)'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fastq: type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - ref: type: file description: | Either "ref" a directory containing an index, the name of another directory with a "ref" subdirectory containing an index or the name of a fasta formatted nucleotide file containg the reference to map to. 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: "versions.yml" - bam: type: file description: BAM file pattern: "*.{bam}" authors: - "@erikrikarddaniel"