Skip to content
GitLab
Explore
Sign in
Register
Primary navigation
Search or go to…
Project
Q
QuaC
Manage
Activity
Members
Labels
Plan
Issues
15
Issue boards
Milestones
Wiki
Code
Merge requests
0
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Package Registry
Container Registry
Model registry
Operate
Environments
Terraform modules
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
This is an archived project. Repository and other project resources are read-only.
Show more breadcrumbs
center-for-computational-genomics-and-data-science
public
QuaC
Commits
9edc03a1
Commit
9edc03a1
authored
3 years ago
by
Manavalan Gajapathy
Browse files
Options
Downloads
Patches
Plain Diff
adds a todo to clean up for testing
parent
70cf53f5
No related branches found
Branches containing commit
No related tags found
Tags containing commit
1 merge request
!2
QC under one umbrella (well mostly) under QuaC
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
workflow/rules/within_species_contamintation.smk
+2
-1
2 additions, 1 deletion
workflow/rules/within_species_contamintation.smk
with
2 additions
and
1 deletion
workflow/rules/within_species_contamintation.smk
+
2
−
1
View file @
9edc03a1
...
...
@@ -26,10 +26,11 @@ rule verifybamid:
params:
svd_prefix=lambda wildcards, input: input["svd"][0].replace(Path(input["svd"][0]).suffix, ""),
out_prefix=lambda wildcards, output: output["ancestry"].replace(".Ancestry", ""),
sanity_check="TODO: Setup --DisableSanityCheck flag for testing dataset",
threads: 4
shell:
r"""
verifybamid2 \
verifybamid2
{params.sanity_check}
\
--NumThread {threads} \
--SVDPrefix {params.svd_prefix} \
--Reference {input.ref_genome} \
...
...
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