version: 1.2
workflows:
   - name: cnv_germline_case_workflow
     subclass: WDL
     primaryDescriptorPath: /scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl
     testParameterFiles:
     -  /scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json
   - name: cnv_germline_cohort_workflow
     subclass: WDL
     primaryDescriptorPath: /scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl
     testParameterFiles:
     -  /scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_workflow.json
   - name: cnv_somatic_pair_workflow
     subclass: WDL
     primaryDescriptorPath: /scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl
     testParameterFiles: 
     -  /scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow.json
   - name: cnv_somatic_panel_workflow
     subclass: WDL
     primaryDescriptorPath: /scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl
     testParameterFiles:
     -  /scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_do-gc_workflow.json
   - name: cram2filtered
     subclass: WDL
     primaryDescriptorPath: /scripts/cnn_variant_wdl/cram2filtered.wdl
     testParameterFiles:
     - /scripts/cnn_variant_wdl/jsons/cram2filtered.json
   - name: cram2model
     subclass: WDL
     primaryDescriptorPath: /scripts/cnn_variant_wdl/cram2model.wdl
     testParameterFiles:
     - /scripts/cnn_variant_wdl/jsons/cram2model.json
   - name: funcotator
     subclass: WDL
     primaryDescriptorPath: /scripts/funcotator_wdl/funcotator.wdl
     testParameterFiles:
     - /scripts/funcotator_wdl/funcotator.json
   - name: MitochondriaPipeline
     subclass: WDL
     primaryDescriptorPath: /scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl
     testParameterFiles:
     -  /scripts/mitochondria_m2_wdl/test_mitochondria_m2_wdl.json
   - name: mutect2
     subclass: WDL
     primaryDescriptorPath: /scripts/mutect2_wdl/mutect2.wdl
     testParameterFiles:
     - /scripts/m2_cromwell_tests/mutect2.inputs.json
   - name: mutect2_pon
     subclass: WDL
     primaryDescriptorPath: /scripts/mutect2_wdl/mutect2_pon.wd
   - name: run_happy
     subclass: WDL
     primaryDescriptorPath: /scripts/cnn_variant_wdl/run_happy.wdl
     testParameterFiles:
     - /scripts/cnn_variant_wdl/jsons/run_happy.json
   - name: pathseq_pipeline
     subclass: WDL
     primaryDescriptorPath: /scripts/pathseq/wdl/pathseq_pipeline.wdl
     testParameterFiles:
     - /scripts/pathseq/wdl/pathseq_pipeline_template.json