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_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"