From 2d3aa1661b68fde2bd57dbebf817041cfb998033 Mon Sep 17 00:00:00 2001 From: Chris Norman Date: Tue, 22 Feb 2022 08:43:54 -0500 Subject: [PATCH] Add companion index to MultiVariantWalker input variant arg. --- .../hellbender/cmdline/StandardArgumentDefinitions.java | 1 + .../MultiVariantInputArgumentCollection.java | 2 ++ 2 files changed, 3 insertions(+) diff --git a/src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java b/src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java index 065759684bb..50dddc82009 100644 --- 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/src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/MultiVariantInputArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/MultiVariantInputArgumentCollection.java index 8f3d52c8867..518ab29da0b 100644 --- a/src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/MultiVariantInputArgumentCollection.java +++ b/src/main/java/org/broadinstitute/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 drivingVariantPaths = new ArrayList<>(); @Override