name: "concoct_concoctcoveragetable"
description: Generate the input coverage table for CONCOCT using a BEDFile
keywords:
  - contigs
  - fragment
  - mags
  - binning
  - bed
  - bam
  - subcontigs
  - coverage
tools:
  - "concoct":
      description: "Clustering cONtigs with COverage and ComposiTion"
      homepage: "https://concoct.readthedocs.io/en/latest/index.html"
      documentation: "https://concoct.readthedocs.io/en/latest/index.html"
      tool_dev_url: "https://github.com/BinPro/CONCOCT"
      doi: "10.1038/nmeth.3103"
      licence: "['FreeBSD']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bed:
      type: file
      description: BED file describing where each contig was cut up (typically output from CONCOCT's cut_up_fasta.py)
      pattern: "*.bed"
  - bamfiles:
      type: file
      description: A single or list of BAM files of reads mapped back to original contigs (prior cutting up)
      pattern: "*.bam"
  - baifiles:
      type: file
      description: A single or list of BAM index files (.bai) corresponding to BAM
      pattern: "*.bam"

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: Contig coverage table
      pattern: "*.tsv"

authors:
  - "@jfy133"
