name: samtools_fastq description: Converts a SAM/BAM/CRAM file to FASTQ keywords: - bam - sam - cram - fastq 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: hhttp://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM/CRAM/SAM file pattern: "*.{bam,cram,sam}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fasta: type: file description: compressed FASTQ file pattern: "*.fastq.gz" - version: type: file description: File containing software version pattern: "versions.yml" authors: - "@suzannejin"