name: samtools_ampliconclip description: Clips read alignments where they match BED file defined regions keywords: - amplicon - clipping - ampliconclip - samtools 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 licence: ["MIT"] 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}" - bed: type: file description: BED file of regions to be removed (e.g. amplicon primers) pattern: "*.{bed}" - save_cliprejects: type: value description: Save filtered reads to a file - save_clipstats: type: value description: Save clipping stats to a file output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - bam: type: file description: Clipped reads BAM file pattern: "*.{bam}" - stats: type: file description: Clipping statistics text file pattern: "*.{clipstats.txt}" - rejects_bam: type: file description: Filtered reads BAM file pattern: "*.{cliprejects.bam}" authors: - "@bjohnnyd"