name: metabat2_jgisummarizebamcontigdepths
description: Depth computation per contig step of metabat2
keywords:
  - sort
  - binning
  - depth
  - bam
  - coverage
  - de novo assembly
tools:
  - metabat2:
      description: Metagenome binning
      homepage: https://bitbucket.org/berkeleylab/metabat/src/master/
      documentation: https://bitbucket.org/berkeleylab/metabat/src/master/
      tool_dev_url: https://bitbucket.org/berkeleylab/metabat/src/master/
      doi: "10.7717/peerj.7359"
      licence: ["BSD-3-clause-LBNL"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: Sorted BAM file of reads aligned on the assembled contigs
      pattern: "*.bam"
  - bai:
      type: file
      description: BAM index file
      pattern: "*.bam.bai"

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:
      type: file
      description: Text file listing the coverage per contig
      pattern: ".txt.gz"

authors:
  - "@maxibor"
