name: "angsd_docounts"
description: Calculates base frequency statistics across reference positions from BAM.
keywords:
  - angsd
  - population genetics
  - allele counts
  - doCounts
tools:
  - "angsd":
      description: "ANGSD: Analysis of next generation Sequencing Data"
      homepage: "http://www.popgen.dk/angsd/"
      documentation: "http://www.popgen.dk/angsd/"
      tool_dev_url: "https://github.com/ANGSD/angsd"
      doi: "10.1186/s12859-014-0356-4"
      licence: "['GPL v3, MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: A list of BAM or CRAM files
      pattern: "*.{bam,cram}"
  - bai:
      type: file
      description: List of BAM/CRAM index files
      pattern: "*.{bai,csi}"
  - minqfile:
      type: file
      description: File with individual quality score thresholds
      pattern: "*"

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"
  - depth_sample:
      type: file
      description: Distribution of sequencing depths
      pattern: "*.depthSample"
  - depth_global:
      type: file
      description: Distribution of sequencing depths
      pattern: "*.depthGlobal"
  - qs:
      type: file
      description: Distribution of scores
      pattern: "*.qs"
  - pos:
      type: file
      description: Various types of depth statistics (depending on value for -dumpCounts)
      pattern: "*.pos.gz"
  - counts:
      type: file
      description: Various types of statistics (related to pos.gz)
      pattern: "*.counts.gz"
  - icounts:
      type: file
      description: Internal format for dumping binary single chrs. Useful for ANGSD contamination
      pattern: "*.icnts.gz"

authors:
  - "@jfy133"