add masked_positions and masked_positions_file arguments to task polyphonia_detect_cross_contamination #499
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
dpark01
requested changes
Dec 11, 2023
pipes/WDL/tasks/tasks_intrahost.wdl
Outdated
| @@ -83,6 +87,8 @@ task polyphonia_detect_cross_contamination { | |||
| ~{'--min-readcount ' + min_readcount} \ | |||
| ~{'--max-mismatches ' + max_mismatches} \ | |||
| ~{'--min-maf ' + min_maf} \ | |||
| ~{'--masked-positions ' + masked_positions} \ | |||
| --masked-positions-file ~{masked_positions_file} \ | |||
There was a problem hiding this comment.
If masked positions file is optional, you should use the same optional parameter syntax as masked positions so it works properly if empty
dpark01
approved these changes
Dec 13, 2023
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Outdated suggestions cannot be applied.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.