Add companion index to MultiVariantWalker input variant arg. (#7689)

broadinstitute · Feb 22, 2022 · 687d93e · 687d93e
1 parent 72530b3
commit 687d93e
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diff --git a/src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java b/src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java
@@ -89,6 +89,7 @@ private StandardArgumentDefinitions(){}
     // Constants for use as companion attributes in WDL WorkflowInput/WorkflowOutput annotations. These values
     // are used by the WDL generator to emit separate task/workflow input and output arguments for companion files.
     public static final String INPUT_INDEX_COMPANION = INPUT_LONG_NAME + "Index";
+    public static final String VARIANT_INDEX_COMPANION = VARIANT_LONG_NAME + "Index";
     public static final String OUTPUT_INDEX_COMPANION = OUTPUT_LONG_NAME + "Index";
     public static final String REFERENCE_INDEX_COMPANION = REFERENCE_LONG_NAME + "Index";
     public static final String REFERENCE_DICTIONARY_COMPANION = REFERENCE_LONG_NAME + "Dictionary";

diff --git a/...institute/hellbender/cmdline/argumentcollections/MultiVariantInputArgumentCollection.java b/...institute/hellbender/cmdline/argumentcollections/MultiVariantInputArgumentCollection.java
@@ -1,6 +1,7 @@
 package org.broadinstitute.hellbender.cmdline.argumentcollections;
 
 import org.broadinstitute.barclay.argparser.Argument;
+import org.broadinstitute.barclay.argparser.WorkflowInput;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.engine.GATKPath;
 import org.broadinstitute.hellbender.engine.MultiVariantWalker;
@@ -28,6 +29,7 @@ public static class DefaultMultiVariantInputArgumentCollection extends MultiVari
         // from any other potential sources of Features.
         @Argument(fullName = StandardArgumentDefinitions.VARIANT_LONG_NAME, shortName = StandardArgumentDefinitions.VARIANT_SHORT_NAME,
                 doc = "One or more VCF files containing variants", common = false, optional = false)
+        @WorkflowInput(optionalCompanions = StandardArgumentDefinitions.VARIANT_INDEX_COMPANION)
         public List<GATKPath> drivingVariantPaths = new ArrayList<>();
 
         @Override