.dockstore.yml

version: 1.2
workflows:
  - name: GiraffeDeepTrio
    subclass: WDL
    description: Core VG Giraffe mapping and DeepTrio calling workflow for maternal-paternal-child sample datasets. It takes as inputs reads in FASTQ and graphs containing the population-based haplotypes to genotype. The graphs files required include the XG, GCSA, GBWT, graph GBWT, Distance and Minimizer indexes. It outputs a VCF file and BAM file for the child along with optional RTG and hap.py vcf evaluation if the user provides benchmark truth-set VCFs.
    primaryDescriptorPath: /workflows/giraffe_and_deeptrio.wdl
    testParameterFiles:
      - /params/vg_hprc_deeptrio_map_call.inputs_tiny.gs_url.json
    branches:
      - master
    authors:
      - name: Charles Markello
        email: cmarkell@ucsc.edu
      - name: Jean Monlong
        email: jmonlong@ucsc.edu
      - name: Adam Novak
        email: anovak@soe.ucsc.edu
  - name: GiraffeDeepVariant
    subclass: WDL
    description: Maps raw short reads from a pair of FASTQs or a CRAM file on a pangenome with vg Giraffe and call variants with DeepVariant.
    primaryDescriptorPath: /workflows/giraffe_and_deepvariant.wdl
    testParameterFiles:
      - /params/giraffe_and_deepvariant.json
    authors:
      - name: Jean Monlong
        email: jmonlong@ucsc.edu
      - name: Adam Novak
        email: anovak@soe.ucsc.edu
      - name: Charles Markello
        email: cmarkell@ucsc.edu
  - name: GiraffeDeepVariantFromGAF
    subclass: WDL
    description: Starts from an aligned GAF file, surject to a linear genome and call variants with DeepVariant.
    primaryDescriptorPath: /workflows/giraffe_and_deepvariant_fromGAF.wdl
    testParameterFiles:
      - /params/giraffe_and_deepvariant_gaf.json
    authors:
      - name: Jean Monlong
        email: jmonlong@ucsc.edu
      - name: Adam Novak
        email: anovak@soe.ucsc.edu
      - name: Charles Markello
        email: cmarkell@ucsc.edu
  - name: Giraffe
    subclass: WDL
    description: Maps raw short reads from a pair of FASTQs or a CRAM file on a pangenome with vg Giraffe.
    primaryDescriptorPath: /workflows/giraffe.wdl
    testParameterFiles:
      - /params/giraffe.json
    authors:
      - name: Jean Monlong
        email: jmonlong@ucsc.edu
      - name: Adam Novak
        email: anovak@soe.ucsc.edu
      - name: Charles Markello
        email: cmarkell@ucsc.edu
  - name: sortGraphAlignedReads
    subclass: WDL
    description: Sort a GAF file
    primaryDescriptorPath: /workflows/sort_graph_aligned_reads.wdl
    testParameterFiles:
      - /params/sort_graph_aligned_reads.gaf.json
    authors:
      - name: Jean Monlong
        email: jmonlong@ucsc.edu
  - name: HappyEvaluation
    subclass: WDL
    description: Evaluate small variants using hap.py
    primaryDescriptorPath: /workflows/happy_evaluation.wdl
    testParameterFiles:
      - /params/happy_evaluation.json
    authors:
      - name: Jean Monlong
        email: jmonlong@ucsc.edu