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