Upgrade CNV WDLs to 1.0 spec (#6506)

broadinstitute · Mar 18, 2020 · 00f1e43 · 00f1e43
1 parent d89c0e6
commit 00f1e43
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Showing 9 changed files with 1,457 additions and 1,395 deletions.
diff --git a/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow_funcotator.json b/scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_do-gc_workflow_funcotator.json
@@ -3,7 +3,7 @@
   "CNVSomaticPairWorkflow.gatk_docker": "__GATK_DOCKER__",
   "CNVSomaticPairWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list",
   "CNVSomaticPairWorkflow.is_run_funcotator": "true",
-  "CNVSomaticPairWorkflow.is_removing_untared_datasources": "true",
+  "CNVSomaticPairWorkflow.funcotator_is_removing_untared_datasources": "true",
   "CNVSomaticPairWorkflow.funcotator_data_sources_tar_gz": "/home/travis/build/broadinstitute/ds.tar.gz",
   "CNVSomaticPairWorkflow.normal_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram",
   "CNVSomaticPairWorkflow.normal_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74NEG-v1-chr20-downsampled.deduplicated.cram.crai",