Make it possible to set java options with picard wrappers. #8
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
Smeds
force-pushed
the
add-javaopt-picard
branch
from
299f9a6
to
b779f20
Compare
johanneskoester
requested changes
Oct 22, 2019
| @@ -6,6 +6,7 @@ rule replace_rg: | |||
| log: | |||
| "logs/picard/replace_rg/{sample}.log" | |||
| params: | |||
| "RGLB=lib1 RGPL=illumina RGPU={sample} RGSM={sample}" | |||
| java_options="-Xmx8g", | |||
There was a problem hiding this comment.
I'd rather like to have this defined as mem_mb resource. This way, we automatically connect this to cluster execution.
|
I think the same thing was implemented across a bunch of Java wrappers in this PR: Feel free to reopen, if anything was missed. |
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Outdated suggestions cannot be applied.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.