Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
T
tasks
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Container Registry
Model registry
Operate
Environments
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
biowdl
tasks
Commits
2aba7899
Commit
2aba7899
authored
4 years ago
by
Cats
Browse files
Options
Downloads
Patches
Plain Diff
increase memory bwa
parent
5db3dd91
No related branches found
Branches containing commit
No related tags found
Tags containing commit
No related merge requests found
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
bwa.wdl
+1
-1
1 addition, 1 deletion
bwa.wdl
with
1 addition
and
1 deletion
bwa.wdl
+
1
−
1
View file @
2aba7899
...
...
@@ -48,7 +48,7 @@ task Mem {
Int estimatedSortThreads = if threads == 1 then 1 else 1 + ceil(threads / 4.0)
Int totalSortThreads = select_first([sortThreads, estimatedSortThreads])
# BWA needs slightly more memory than the size of the index files (~10%). Add a margin for safety here.
Int estimatedMemoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G") *
2
) + sortMemoryPerThreadGb * totalSortThreads
Int estimatedMemoryGb = 1
0
+ ceil(size(bwaIndex.indexFiles, "G") *
3
) + sortMemoryPerThreadGb * totalSortThreads
# The bwa postalt script is out commented as soon as usePostalt = false.
# This hack was tested with bash, dash and ash. It seems that comments in between pipes work for all of them.
...
...
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment