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 licence: ["GPL-3.0-or-later"] 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 ] - versions: type: file description: File containing software versions pattern: "versions.yml" - seqz: type: file description: Seqz file pattern: "*.{seqz.gz}" authors: - "@kaurravneet4123"