Handle records with empty EVIDENCE field in MakeCohortVcf (#233)

* and add terra pipeline diagram to terra dashboard
broadinstitute · Sep 17, 2021 · cd90dc4 · cd90dc4
1 parent a1a13e3
commit cd90dc4
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diff --git a/input_templates/terra_workspaces/cohort_mode/cohort_mode_workspace_dashboard.md.tmpl b/input_templates/terra_workspaces/cohort_mode/cohort_mode_workspace_dashboard.md.tmpl
@@ -47,6 +47,8 @@ The following are the main pipeline outputs. For more information on the outputs
 
 ### Pipeline overview
 
+<img alt="pipeline_diagram" title="Pipeline diagram" src="https://github.com/broadinstitute/gatk-sv/blob/v0.18.1-beta/terra_pipeline_diagram.jpg?raw=true" width="1000">
+
 The following workflows are included in this workspace, to be executed in this order:
 
 1. `01-GatherSampleEvidence`: Per-sample SV evidence collection, including calls from a configurable set of algorithms (Delly, Manta, MELT, and Wham), read depth (RD), split read positions (SR), and discordant pair positions (PE).

diff --git a/input_values/dockers.json b/input_values/dockers.json
@@ -13,7 +13,7 @@
   "sv_base_docker" : "us.gcr.io/broad-dsde-methods/markw/sv-base:mw-gnomad-0506-pr-087d4df",
   "sv_base_mini_docker" : "us.gcr.io/broad-dsde-methods/markw/sv-base-mini:mw-gnomad-0506-pr-087d4df",
   "sv_pipeline_base_docker" : "us.gcr.io/broad-dsde-methods/markw/sv-pipeline-base:mw-gnomad-0506-pr-087d4df",
-  "sv_pipeline_docker" : "us.gcr.io/broad-dsde-methods/eph/sv-pipeline:eph_mediancov_mem_and_names-3f0c76d",
+  "sv_pipeline_docker" : "us.gcr.io/broad-dsde-methods/eph/sv-pipeline:eph_hotfix_no_evidence-1f461ed",
   "sv_pipeline_qc_docker" : "us.gcr.io/broad-dsde-methods/markw/sv-pipeline-qc:mw-gnomad-0506-pr-087d4df",
   "sv_pipeline_rdtest_docker" : "us.gcr.io/broad-dsde-methods/markw/sv-pipeline-rdtest:mw-gnomad-0506-pr-087d4df",
   "wham_docker" : "us.gcr.io/broad-dsde-methods/wham:8645aa",

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/overlap_breakpoint_filter.py b/src/sv-pipeline/04_variant_resolution/scripts/overlap_breakpoint_filter.py
@@ -40,6 +40,8 @@ def __init__(self, record):
             self.level_of_support = 6
         elif 'SR' in ev:
             self.level_of_support = 7
+        elif len(ev) == 0:
+            self.level_of_support = 8
         else:
             raise ValueError("Uninterpretable evidence: {}".format(ev))
         if record.id in bothside_pass:

diff --git a/terra_pipeline_diagram.jpg b/terra_pipeline_diagram.jpg