nf-core_modules/modules/freebayes/germline/meta.yml
FriederikeHanssen 3df4fe6085
add freebayes/somatic and update freebayes/germline (#990)
* add freebayes/somatic and update freebayes/germline to new syntax and cram

* add pytest

* update with new freebayes/germline path
2021-10-29 17:05:06 +02:00

78 lines
2.1 KiB
YAML

name: freebayes_germline
description: A haplotype-based variant detector
keywords:
- variant caller
- SNP
- genotyping
- variant calling
- bayesian
tools:
- freebayes:
description: Bayesian haplotype-based polymorphism discovery and genotyping
homepage: https://github.com/freebayes/freebayes
documentation: https://github.com/freebayes/freebayes
tool_dev_url: https://github.com/freebayes/freebayes
doi: "arXiv:1207.3907"
licence: ['MIT']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- input_index:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.bam.bai"
- fasta:
type: file
description: reference fasta file
pattern: ".{fa,fa.gz,fasta,fasta.gz}"
- fai:
type: file
description: reference fasta file index
pattern: "*.fai"
- targets:
type: file
description: Optional - Limit analysis to targets listed in this BED-format FILE.
pattern: "*.bed"
- samples:
type: file
description: Optional - Limit analysis to samples listed (one per line) in the FILE.
pattern: "*.txt"
- populations:
type: file
description: Optional - Each line of FILE should list a sample and a population which it is part of.
pattern: "*.txt"
- cnv:
type: file
description: |
A copy number map BED file, which has
either a sample-level ploidy:
sample_name copy_number
or a region-specific format:
seq_name start end sample_name copy_number
pattern: "*.bed"
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: "*.{version.txt}"
- vcf:
type: file
description: Compressed VCF file
pattern: "*.vcf.gz"
authors:
- "@maxibor"
- "@FriederikeHanssen"