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Add companion index to MultiVariantWalker input variant arg. #7689

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Feb 22, 2022
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Add companion index to MultiVariantWalker input variant arg. #7689

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1 change: 1 addition & 0 deletions src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java
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Expand Up @@ -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";
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2 changes: 2 additions & 0 deletions ...institute/hellbender/cmdline/argumentcollections/MultiVariantInputArgumentCollection.java
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@@ -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;
Expand Down Expand Up @@ -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
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