name: "smncopynumbercaller"
description: tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file.
keywords:
  - copy number, BAM, CRAM, SMN1, SMN2
tools:
  - "smncopynumbercaller":
      description: "call copy number of SMN1, SMN2, SMN2Δ7–8 from a bam file"
      homepage: "https://github.com/Illumina/SMNCopyNumberCaller"
      documentation: "https://github.com/Illumina/SMNCopyNumberCaller"
      tool_dev_url: "https://github.com/Illumina/SMNCopyNumberCaller"
      doi: "10.1038/s41436-020-0754-0"
      licence: "Apache License Version 2.0"

input:
  - bam:
      type: file
      description: BAM/CRAM file
      pattern: "*.{bam,cram}"
  - bai:
      type: file
      description: BAM/CRAM index file
      pattern: "*.{bai,crai}"
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - run_metrics:
      type: file
      description: File containing run parameters of SMNCopyNumberCaller
      pattern: "*.{json}"
  - smncopynumber:
      type: file
      description: File containing the output of SMNCopyNumberCaller
      pattern: "*.{tsv}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@peterpru"
