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257078bb39
* add BP to strelka/somatic * merge conflicts * update strelka modules for BP * update strelka modules for BP * apply suggestions from code review
93 lines
2.7 KiB
YAML
93 lines
2.7 KiB
YAML
name: strelka_somatic
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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
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keywords:
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- variant calling
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- germline
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- wgs
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- vcf
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- variants
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tools:
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- strelka:
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description: Strelka calls somatic and germline small variants from mapped sequencing reads
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homepage: https://github.com/Illumina/strelka
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documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md
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tool_dev_url: https://github.com/Illumina/strelka
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doi: 10.1038/s41592-018-0051-x
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licence: ['GPL v3']
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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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- cram_normal:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- crai_normal:
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type: file
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description: BAM/CRAM/SAM index file
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pattern: "*.{bai,crai,sai}"
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- cram_tumor:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- crai_tumor:
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type: file
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description: BAM/CRAM/SAM index file
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pattern: "*.{bai,crai,sai}"
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- manta_candidate_small_indels:
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type: file
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description: VCF.gz file
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pattern: "*.{vcf.gz}"
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- manta_candidate_small_indels_tbi:
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type: file
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description: VCF.gz index file
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pattern: "*.tbi"
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- fasta:
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type: file
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description: Genome reference FASTA file
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pattern: "*.{fa,fasta}"
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- fai:
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type: file
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description: Genome reference FASTA index file
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pattern: "*.{fa.fai,fasta.fai}"
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- target_bed:
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type: file
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description: BED file containing target regions for variant calling
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pattern: "*.{bed}"
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- target_bed_tbi:
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type: file
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description: Index for BED file containing target regions for variant calling
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pattern: "*.{bed.tbi}"
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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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- vcf_indels:
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type: file
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description: Gzipped VCF file containing variants
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pattern: "*.{vcf.gz}"
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- vcf_indels_tbi:
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type: file
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description: Index for gzipped VCF file containing variants
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pattern: "*.{vcf.gz.tbi}"
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- vcf_snvs:
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type: file
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description: Gzipped VCF file containing variants
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pattern: "*.{vcf.gz}"
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- vcf_snvs_tbi:
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type: file
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description: Index for gzipped VCF file containing variants
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pattern: "*.{vcf.gz.tbi}"
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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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authors:
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- "@drpatelh"
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