name: "concoct_mergecutupclustering"
description: Merge consecutive parts of the original contigs original cut up by cut_up_fasta.py
keywords:
  - contigs
  - fragment
  - mags
  - binning
  - fasta
  - cut
  - cut up
  - merge
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 ]
  - clustering_csv:
      type: file
      description: Input cutup clustering result. Typically *_gt1000.csv from concoct
      pattern: "*.csv"

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"
  - csv:
      type: file
      description: Cluster assignments per contig part with concensus cluster
      pattern: "*.csv"

authors:
  - "@jfy133"
