mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
85 lines
2.5 KiB
YAML
85 lines
2.5 KiB
YAML
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 ]
|
|
- cram_normal:
|
|
type: file
|
|
description: BAM/CRAM/SAM file
|
|
pattern: "*.{bam,cram,sam}"
|
|
- crai_normal:
|
|
type: file
|
|
description: BAM/CRAM/SAM index file
|
|
pattern: "*.{bai,crai,sai}"
|
|
- cram_tumor:
|
|
type: file
|
|
description: BAM/CRAM/SAM file
|
|
pattern: "*.{bam,cram,sam}"
|
|
- crai_tumor:
|
|
type: file
|
|
description: BAM/CRAM/SAM index file
|
|
pattern: "*.{bai,crai,sai}"
|
|
- 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_tbi:
|
|
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"
|