nf-core_modules/modules/sequenzautils/bam2seqz/meta.yml

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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"