Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

freebayes selector still used old sw name #837

Merged
merged 1 commit into from
Nov 15, 2022
Merged

freebayes selector still used old sw name #837

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#814](https://github.com/nf-core/sarek/pull/814) - Fix readgroups when using DragMap together with FreeBayes or Mutect2 (see issue [#780](https://github.com/nf-core/sarek/issues/780))
- [#817](https://github.com/nf-core/sarek/pull/817) - Fix CNVKit run on tumor-only sample to be run on all samples
- [#828](https://github.com/nf-core/sarek/pull/817) - Fix issue [#763](https://github.com/nf-core/sarek/issues/763) to run variantcalling when starting form step recalibration
- [#837](https://github.com/nf-core/sarek/pull/837) - Fix Freebayes config selector after subworkflow renaming

### Deprecated

Expand Down
2 changes: 1 addition & 1 deletion conf/modules/freebayes.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ process {

// PAIR_VARIANT_CALLING
if (params.tools && params.tools.split(',').contains('freebayes')) {
withName: '.*:PAIR_VARIANT_CALLING:RUN_FREEBAYES_SOMATIC:FREEBAYES' {
withName: '.*:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_FREEBAYES:FREEBAYES' {
ext.args = "--pooled-continuous \
--pooled-discrete \
--genotype-qualities \
Expand Down