Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add companion index to MultiVariantWalker input variant arg. #7689

Merged
merged 1 commit into from
Feb 22, 2022
Merged

Add companion index to MultiVariantWalker input variant arg. #7689

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java
View file
Open in desktop
Original file line number Diff line number Diff line change
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";
Expand Down
2 changes: 2 additions & 0 deletions ...institute/hellbender/cmdline/argumentcollections/MultiVariantInputArgumentCollection.java
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -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
Expand Down