name: samtools_faidx description: Index FASTA file keywords: - index - fasta tools: - samtools: description: | SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. homepage: http://www.htslib.org/ documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fasta: type: file description: FASTA file pattern: "*.{fa,fasta}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fai: type: file description: FASTA index file pattern: "*.{fai}" - gzi: type: file description: Optional gzip index file for compressed inputs pattern: "*.gzi" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" - "@phue"