1version: 1.2 2workflows: 3 - name: cnv_germline_case_workflow 4 subclass: WDL 5 primaryDescriptorPath: /scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl 6 testParameterFiles: 7 - /scripts/cnv_cromwell_tests/germline/cnv_germline_case_scattered_workflow.json 8 - name: cnv_germline_cohort_workflow 9 subclass: WDL 10 primaryDescriptorPath: /scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl 11 testParameterFiles: 12 - /scripts/cnv_cromwell_tests/germline/cnv_germline_cohort_workflow.json 13 - name: cnv_somatic_pair_workflow 14 subclass: WDL 15 primaryDescriptorPath: /scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl 16 testParameterFiles: 17 - /scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow.json 18 - name: cnv_somatic_panel_workflow 19 subclass: WDL 20 primaryDescriptorPath: /scripts/cnv_wdl/somatic/cnv_somatic_panel_workflow.wdl 21 testParameterFiles: 22 - /scripts/cnv_cromwell_tests/somatic/cnv_somatic_panel_wes_do-gc_workflow.json 23 - name: cram2filtered 24 subclass: WDL 25 primaryDescriptorPath: /scripts/cnn_variant_wdl/cram2filtered.wdl 26 testParameterFiles: 27 - /scripts/cnn_variant_wdl/jsons/cram2filtered.json 28 - name: cram2model 29 subclass: WDL 30 primaryDescriptorPath: /scripts/cnn_variant_wdl/cram2model.wdl 31 testParameterFiles: 32 - /scripts/cnn_variant_wdl/jsons/cram2model.json 33 - name: funcotator 34 subclass: WDL 35 primaryDescriptorPath: /scripts/funcotator_wdl/funcotator.wdl 36 testParameterFiles: 37 - /scripts/funcotator_wdl/funcotator.json 38 - name: MitochondriaPipeline 39 subclass: WDL 40 primaryDescriptorPath: /scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl 41 testParameterFiles: 42 - /scripts/mitochondria_m2_wdl/test_mitochondria_m2_wdl.json 43 - name: mutect2 44 subclass: WDL 45 primaryDescriptorPath: /scripts/mutect2_wdl/mutect2.wdl 46 testParameterFiles: 47 - /scripts/m2_cromwell_tests/mutect2.inputs.json 48 - name: mutect2_pon 49 subclass: WDL 50 primaryDescriptorPath: /scripts/mutect2_wdl/mutect2_pon.wd 51 - name: run_happy 52 subclass: WDL 53 primaryDescriptorPath: /scripts/cnn_variant_wdl/run_happy.wdl 54 testParameterFiles: 55 - /scripts/cnn_variant_wdl/jsons/run_happy.json 56 - name: pathseq_pipeline 57 subclass: WDL 58 primaryDescriptorPath: /scripts/pathseq/wdl/pathseq_pipeline.wdl 59 testParameterFiles: 60 - /scripts/pathseq/wdl/pathseq_pipeline_template.json 61