nf-core_modules/modules/vardictjava/meta.yml
nvnieuwk eab173f2bb
Added java options to vardict java (#1695)
* Added java options to vardict java

* updated test.yml

* correctly added java options

* Added automatic version numbers for vardictjava

* possible fix for version number in conda

* removed the cram tests

* linting

* Update modules/vardictjava/main.nf

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

* Update modules/vardictjava/main.nf

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

* removed the version line

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-08-10 14:13:03 +02:00

60 lines
1.5 KiB
YAML

name: "vardictjava"
description: The Java port of the VarDict variant caller
keywords:
- variant calling
- VarDict
- AstraZeneca
tools:
- "vardictjava":
description: "Java port of the VarDict variant discovery program"
homepage: "https://github.com/AstraZeneca-NGS/VarDictJava"
documentation: "https://github.com/AstraZeneca-NGS/VarDictJava"
tool_dev_url: "https://github.com/AstraZeneca-NGS/VarDictJava"
doi: "10.1093/nar/gkw227 "
licence: "['MIT']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/SAM file
pattern: "*.{bam,sam}"
- bai:
type: file
description: Index of the BAM file
pattern: "*.bai"
- bed:
type: file
description: BED with the regions of interest
pattern: "*.bed"
- fasta:
type: file
description: FASTA of the reference genome
pattern: "*.{fa,fasta}"
- fasta_fai:
type: file
description: The index of the FASTA of the reference genome
pattern: "*.fai"
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"
- vcf:
type: file
description: VCF file output
pattern: "*.vcf.gz"
authors:
- "@nvnieuwk"