# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
name: "fasta_binning_concoct"
description: Runs the CONCOCT workflow of contig binning
keywords:
  - concoct
  - binning
  - metagenomics
  - contigs
components:
  - concoct/cutupfasta
  - concoct/concoctcoveragetable
  - concoct/concoct
  - concoct/mergecutupclustering
  - concoct/extractfastabins
input:
  - ch_fasta:
      type: file
      description: |
        Structure: [ val(meta), path(fasta)]
        File containing raw assembled contigs in FASTA format.
  - ch_bam:
      type: file
      description: |
        Structure: [ val(meta), path(bam), path(bai)]
        BAM and associated index files file representing reads mapped against each
        contig in ch_fasta. Meta must be identical between ch_fasta and ch_bam entries.

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - coverage_table:
      type: file
      description: |
        Structure: [ val(meta), path(tsv)]
        (Sub)contig coverage table
  - original_csv:
      type: file
      description: |
        Structure: [ val(meta), path(csv) ]
        Original CONCOCT GT1000 output
  - raw_clustering_csv:
      type: file
      description: |
        Structure: [ val(meta), path(csv) ]
        CSV containing information which subcontig is assigned to which cluster
  - pca_original:
      type: file
      description: |
        Structure: [ val(meta), path(csv) ]
        CSV file containing untransformed PCA component values
  - pca_transformed:
      type: file
      description: |
        Structure: [ val(meta), path(csv) ]
        CSV file transformed PCA component values
  - cluster_table:
      type: file
      description: |
        Structure: [ val(meta), path(csv) ]
        CSV file containing final cluster assignments of original input contigs
  - bin:
      type: file
      description: |
        Structure: [ val(meta), path(fasta) ]
        FASTA files containing CONCOCT predicted bin clusters, named numerically
        by CONCOCT cluster ID
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@jfy133"
