---
name: "ngsbits_samplegender"
description: Determines the gender of a sample from the BAM/CRAM file.
keywords:
  - gender
  - cram
  - bam
  - short reads
tools:
  - "ngsbits":
      description: "Short-read sequencing tools"
      homepage: "https://github.com/imgag/ngs-bits"
      documentation: "https://github.com/imgag/ngs-bits"
      tool_dev_url: "https://github.com/imgag/ngs-bits"
      licence: "['MIT license']"
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: One or more BAM/CRAM files to determine the gender of
      pattern: "*.{bam,cram}"
  - bai:
      type: file
      description: The index file(s) from the input BAM/CRAM file(s)
      pattern: "*.{bai,crai}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference fasta information
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: The reference FASTA to use (mandatory when CRAM files are used)
      pattern: "*.{fasta,fa,fna}"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference fasta index information
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: The index of the reference FASTA to use (mandatory when CRAM files are used)
      pattern: "*.fai"
  - method:
      type: string
      description: The method to use to define the gender (posibilities are 'xy', 'hetx' and 'sry')
      pattern: "(xy|hetx|sry)"
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"
  - tsv:
      type: file
      description: An output TSV file containing the results of the gender prediction
      pattern: "*.tsv"
authors:
  - "@nvnieuwk"
maintainers:
  - "@nvnieuwk"
