name: ataqv_ataqv
description: ataqv function of a corresponding ataqv tool
keywords:
  - ataqv
tools:
  - ataqv:
      description: ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing.
      homepage: https://github.com/ParkerLab/ataqv/blob/master/README.rst
      documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst
      tool_dev_url: https://github.com/ParkerLab/ataqv
      doi: "https://doi.org/10.1016/j.cels.2020.02.009"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM file
      pattern: "*.bam"
  - bai:
      type: file
      description: BAM index file with the same prefix as bam file. Required if tss_file input is provided.
      pattern: "*.bam.bai"
  - peak_file:
      type: file
      description: A BED file of peaks called for alignments in the BAM file
      pattern: "*.bed"
  - organism:
      type: string
      description: The subject of the experiment, which determines the list of autosomes (see "Reference Genome Configuration" section at https://github.com/ParkerLab/ataqv).
  - mito_name:
      type: string
      description: Name of the mitochondrial sequence.
  - tss_file:
      type: file
      description: A BED file of transcription start sites for the experiment organism. If supplied, a TSS enrichment score will be calculated according to the ENCODE data standards. This calculation requires that the BAM file of alignments be indexed.
      pattern: "*.bed"
  - excl_regs_file:
      type: file
      description: A BED file containing excluded regions. Peaks or TSS overlapping these will be ignored.
      pattern: "*.bed"
  - autosom_ref_file:
      type: file
      description: A file containing autosomal reference names, one per line. The names must match the reference names in the alignment file exactly, or the metrics based on counts of autosomal alignments will be wrong.

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - json:
      type: file
      description: The JSON file to which metrics will be written.
  - problems:
      type: file
      description: If given, problematic reads will be logged to a file per read group, with names derived from the read group IDs, with ".problems" appended. If no read groups are found, the reads will be written to one file named after the BAM file.
      pattern: "*.problems"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@i-pletenev"
