name: chromap_chromap
description: |
  Performs preprocessing and alignment of chromatin fastq files to
  fasta reference files using chromap.
keywords:
  - chromap
  - alignment
  - map
  - fastq
  - bam
  - sam
  - hi-c
  - atac-seq
  - chip-seq
  - trimming
  - duplicate removal
tools:
  - chromap:
      description: Fast alignment and preprocessing of chromatin profiles
      homepage: https://github.com/haowenz/chromap
      documentation: https://github.com/haowenz/chromap
      tool_dev_url: https://github.com/haowenz/chromap

      licence: ["GPL v3"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
        respectively.
  - meta2:
      type: map
      description: |
        Groovy Map containing information for the fasta
        e.g. [ id:'test' ]
  - fasta:
      type: file
      description: |
        The fasta reference file.
  - meta3:
      type: map
      description: |
        Groovy Map containing information for the index
        e.g. [ id:'test' ]
  - index:
      type: file
      description: |
        Chromap genome index files (*.index)
  - barcodes:
      type: file
      description: |
        Cell barcode files
  - whitelist:
      type: file
      description: |
        Cell barcode whitelist file
  - chr_order:
      type: file
      description: |
        Custom chromosome order
  - pairs_chr_order:
      type: file
      description: |
        Natural chromosome order for pairs flipping
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"
  - bed:
      type: file
      description: BED file
      pattern: "*.bed.gz"
  - bam:
      type: file
      description: BAM file
      pattern: "*.bam"
  - tagAlign:
      type: file
      description: tagAlign file
      pattern: "*.tagAlign.gz"
  - pairs:
      type: file
      description: pairs file
      pattern: "*.pairs.gz"

authors:
  - "@mahesh-panchal"
  - "@joseespinosa"
