name: manta_germline
description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
keywords:
  - somatic
  - wgs
  - wxs
  - panel
  - vcf
  - structural variants
  - small indels
tools:
  - manta:
      description: Structural variant and indel caller for mapped sequencing data
      homepage: https://github.com/Illumina/manta
      documentation: https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md
      tool_dev_url: https://github.com/Illumina/manta
      doi: "10.1093/bioinformatics/btv710"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - input:
      type: file
      description: BAM/CRAM/SAM file. For joint calling use a list of files.
      pattern: "*.{bam,cram,sam}"
  - index:
      type: file
      description: BAM/CRAM/SAM index file. For joint calling use a list of files.
      pattern: "*.{bai,crai,sai}"
  - 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}"
  - meta2:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fasta:
      type: file
      description: Genome reference FASTA file
      pattern: "*.{fa,fasta}"
  - meta3:
      type: map
      description: |
        Groovy Map containing reference information
        e.g. [ id:'genome' ]
  - fai:
      type: file
      description: Genome reference FASTA index file
      pattern: "*.{fa.fai,fasta.fai}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - candidate_small_indels_vcf:
      type: file
      description: Gzipped VCF file containing variants
      pattern: "*.{vcf.gz}"
  - candidate_small_indels_vcf_tbi:
      type: file
      description: Index for gzipped VCF file containing variants
      pattern: "*.{vcf.gz.tbi}"
  - candidate_sv_vcf:
      type: file
      description: Gzipped VCF file containing variants
      pattern: "*.{vcf.gz}"
  - candidate_sv_vcf_tbi:
      type: file
      description: Index for gzipped VCF file containing variants
      pattern: "*.{vcf.gz.tbi}"
  - diploid_sv_vcf:
      type: file
      description: Gzipped VCF file containing variants
      pattern: "*.{vcf.gz}"
  - diploid_sv_vcf_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:
  - "@maxulysse"
  - "@ramprasadn"
