.dockstore.yml

version: 1.2

workflows:
  - name: cnn-variant-filter
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/cnn-variant-filter.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
  - name: RNA_aggregate
    subclass: WDL
    publish: True
    primaryDescriptorPath: /RNA_pipeline/RNA_aggregate.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
  - name: RNA_pipeline
    subclass: WDL
    publish: True
    primaryDescriptorPath: /RNA_pipeline/RNA_pipeline.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - update-rna-pipeline-for-crams
  - name: WGS_pipeline
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/WGS_pipeline.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - guidemat-wdl
  - name: WGS_aggregate
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/WGS_aggregate.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
  - name: rnaseq_mutect2_tumor_only
    subclass: WDL
    publish: True
    primaryDescriptorPath: /RNA_pipeline/rnaseq_mutect2_tumor_only.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
  - name: rsem_depmap
    subclass: WDL
    publish: True
    primaryDescriptorPath: /RNA_pipeline/rsem_depmap.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - rsem_confidence_interval_calculation
  - name: opencravat
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/opencravat.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - finishing_mutation_pipeline
  - name: bcftools_setGT
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/bcftools.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - finishing_mutation_pipeline
  - name: fix_mutect2col
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/fix_mutect2col.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - finishing_mutation_pipeline
  - name: omics_mutect2
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/omics_mutect2.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - finishing_mutation_pipeline
  - name: manta_annot
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/manta_annot.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - finishing_mutation_pipeline
  - name: Manta_SomaticSV
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/Manta_SomaticSV.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - finishing_mutation_pipeline
  - name: fix_mutect2_clust
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/fix_mutect2_clust.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - finishing_mutation_pipeline
  - name: merge_mutect2_replicates
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/merge_mutect2_replicates.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - finishing_mutation_pipeline
  - name: filter_to_maf
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/filter_to_maf.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - finishing_mutation_pipeline
  - name: merge_and_upload
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/merge_and_upload.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - finishing_mutation_pipeline
  - name: omics_post_mutect2
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/omics_post_mutect2.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - finishing_mutation_pipeline
  - name: opencravat_dm
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/opencravat_dm.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - add-cosmic-to-oc
        - add-oncokb-to-oc
  - name: vcf_to_depmap
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/vcf_to_depmap.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - dev
        - master
        - mutation-annotation-eval
        - update-vcf-to-depmap
        - add-tert-to-wdl
        - add-aplice-ai
        - tcga_mutation_processing
  - name: vcf2maf
    subclass: WDL
    publish: True
    primaryDescriptorPath: /sandbox/vcf2maf/vcf2maf.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - qq-vcf2maf-test
  - name: hgvs
    subclass: WDL
    publish: True
    primaryDescriptorPath: /sandbox/hgvs/hgvs.wdl
    testParameterFiles:
      - /sandbox/hgvs/test.json
    filters: # All tags, no branches
      branches:
        - dev-hgvs
  - name: rna_index
    subclass: WDL
    publish: True
    primaryDescriptorPath: /sandbox/build_rna_idx/rna_index.wdl
    testParameterFiles:
      - /sandbox/build_rna_idx/test.json
    filters: # All tags, no branches
      branches:
        - master
  - name: telomere
    subclass: WDL
    publish: True
    primaryDescriptorPath: /sandbox/telomere/telomerehunter.wdl
    testParameterFiles:
      - /sandbox/telomere/test.json
    filters: # All tags, no branches
      branches:
        - devel-telomere
  - name: rsem_aggregate_results
    subclass: WDL
    publish: True
    primaryDescriptorPath: /RNA_pipeline/rsem_aggregate_results.wdl
    filters:
      branches:
        - add-effective-length
        - master
  - name: annotate_variants
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/annotate_variants.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - merge-annotators
        - master
        - dev-hgvs
        - tcga_mutation_processing
  - name: WGS_preprocessing_DRAGEN_24Q2
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/WGS_preprocessing_DRAGEN_24Q2.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - master
  - name: mask_variants
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/mask_variants.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - mask-repeats-and-segdups
  - name: aggregate_microsatellite_repeats
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/aggregate_microsatellite_repeats.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - microsat
  - name: wgs_qc
    subclass: WDL
    publish: True
    primaryDescriptorPath: /sandbox/wgs_qc/workflow.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - add-wgs-cram-qc
  - name: guide_mutation_binary
    subclass: WDL
    publish: True
    primaryDescriptorPath: /sandbox/guidemat/guide_mutation_binary.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - guidemat-wdl
  # - name: CramToBam
  #   subclass: WDL
  #   publish: True
  #   primaryDescriptorPath: /WGS_pipeline/CramToBam.wdl
  #   testParameterFiles:
  #     - /test.json
  #   filters: # All tags, no branches
  #     branches:
  #       - master
  # - name: BamToUnmappedRGBams_noHardClips
  #   subclass: WDL
  #   publish: True
  #   primaryDescriptorPath: /WGS_pipeline/BamToUnmappedRGBams_noHardClips.wdl
  #   testParameterFiles:
  #     - /test.json
  #   filters: # All tags, no branches
  #     branches:
  #       - master
  - name: vep_sv
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/vep_sv.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - vep-sv
  - name: Manta_SomaticSV_v1_0
    subclass: WDL
    publish: True
    primaryDescriptorPath: /WGS_pipeline/Manta_SomaticSV_v1_0.wdl
    testParameterFiles:
      - /test.json
    filters: # All tags, no branches
      branches:
        - vep-sv