name: sequenzautils_bam2seqz
description: Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file
keywords:
  - bam2seqz
tools:
  - sequenzautils:
      description: Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies.
      homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html
      documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html
      doi: 10.1093/annonc/mdu479

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - normalbam:
      type: file
      description: BAM file from the reference/normal sample
      pattern: "*.{bam}"
  - tumourbam:
      type: file
      description: BAM file from the tumour sample
      pattern: "*.{bam}"
  - fasta:
      type: file
      description: Reference FASTA file
      pattern: "*.{fasta}"
  - wigfile:
      type: file
      description: GC content wiggle file
      pattern: "*.{wig.gz}"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - version:
      type: file
      description: File containing software version
      pattern: "versions.yml"
  - seqz:
      type: file
      description: Seqz file
      pattern: "*.{seqz.gz}"

authors:
  - "@kaurravneet4123"