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meta.yml
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meta.yml
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name: strelka_somatic
description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs
keywords:
- variant calling
- germline
- wgs
- vcf
- variants
tools:
- strelka:
description: Strelka calls somatic and germline small variants from mapped sequencing reads
homepage: https://github.com/Illumina/strelka
documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md
tool_dev_url: https://github.com/Illumina/strelka
doi: 10.1038/s41592-018-0051-x
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input_normal:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- input_index_normal:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
- input_tumor:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- input_index_tumor:
type: file
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
- manta_candidate_small_indels:
type: file
description: VCF.gz file
pattern: "*.{vcf.gz}"
- manta_candidate_small_indels_tbi:
type: file
description: VCF.gz index file
pattern: "*.tbi"
- fasta:
type: file
description: Genome reference FASTA file
pattern: "*.{fa,fasta}"
- fai:
type: file
description: Genome reference FASTA index file
pattern: "*.{fa.fai,fasta.fai}"
- target_bed:
type: file
description: BED file containing target regions for variant calling
pattern: "*.{bed}"
- target_bed_index:
type: file
description: Index for BED file containing target regions for variant calling
pattern: "*.{bed.tbi}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- vcf_indels:
type: file
description: Gzipped VCF file containing variants
pattern: "*.{vcf.gz}"
- vcf_indels_tbi:
type: file
description: Index for gzipped VCF file containing variants
pattern: "*.{vcf.gz.tbi}"
- vcf_snvs:
type: file
description: Gzipped VCF file containing variants
pattern: "*.{vcf.gz}"
- vcf_snvs_tbi:
type: file
description: Index for gzipped VCF file containing variants
pattern: "*.{vcf.gz.tbi}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@drpatelh"
maintainers:
- "@drpatelh"