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eab173f2bb
* 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>
60 lines
1.5 KiB
YAML
60 lines
1.5 KiB
YAML
name: "vardictjava"
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description: The Java port of the VarDict variant caller
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keywords:
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- variant calling
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- VarDict
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- AstraZeneca
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tools:
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- "vardictjava":
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description: "Java port of the VarDict variant discovery program"
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homepage: "https://github.com/AstraZeneca-NGS/VarDictJava"
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documentation: "https://github.com/AstraZeneca-NGS/VarDictJava"
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tool_dev_url: "https://github.com/AstraZeneca-NGS/VarDictJava"
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doi: "10.1093/nar/gkw227 "
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licence: "['MIT']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: BAM/SAM file
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pattern: "*.{bam,sam}"
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- bai:
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type: file
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description: Index of the BAM file
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pattern: "*.bai"
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- bed:
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type: file
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description: BED with the regions of interest
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pattern: "*.bed"
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- fasta:
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type: file
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description: FASTA of the reference genome
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pattern: "*.{fa,fasta}"
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- fasta_fai:
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type: file
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description: The index of the FASTA of the reference genome
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pattern: "*.fai"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- vcf:
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type: file
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description: VCF file output
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pattern: "*.vcf.gz"
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authors:
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- "@nvnieuwk"
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