Match format of filename output in GvsRescatterCallsetInterval #7539
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
Travis reported job failures from build 36661
|
ahaessly
approved these changes
Nov 3, 2021
| @@ -12,7 +12,7 @@ workflow GvsRescatterCallsetInterval { | |||
| File reference | |||
| File reference_dict | |||
| File reference_index | |||
| String final_output_gcs_dir | |||
| String? final_output_gcs_dir | |||
There was a problem hiding this comment.
this gets passed into merge vcfs. do we know whether this works if it is not specified?
$(echo ~{output_directory} | sed 's//$//')
There was a problem hiding this comment.
I tested it and it's the same technique used in GvsExtractCallset (see https://github.com/broadinstitute/gatk/blob/ah_var_store/scripts/variantstore/wdl/GvsExtractCallset.wdl#L214)
This was referenced Mar 17, 2023
Closed
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.