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"