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

Fix 267 #279

Merged
merged 2 commits into from
Sep 2, 2020
Merged

Fix 267 #279

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
8a4e237
fix issue with --step prepare_recalibration #267
maxulysse Sep 1, 2020
6db85c1
update CHANGELOG
maxulysse Sep 1, 2020
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 @@ -24,6 +24,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)

- [#229](https://github.com/nf-core/sarek/pull/229) - Fix `Control-FREEC` restart issue [#225](https://github.com/nf-core/sarek/issues/225)
- [#236](https://github.com/nf-core/sarek/pull/236) - Fix `Mutect2` typo issue [#227](https://github.com/nf-core/sarek/issues/227)
- [#279](https://github.com/nf-core/sarek/pull/279) - Fix issue with `--step prepare_recalibration` [#267](https://github.com/nf-core/sarek/issues/267)

### Removed

Expand Down
2 changes: 1 addition & 1 deletion main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1951,7 +1951,7 @@ bamQCReport = bamQCReport.dump(tag:'BamQC')
if (params.sentieon && step == 'mapping') bam_recalibrated = bam_sentieon_recal

// When no knownIndels for mapping, Channel bam_recalibrated is bam_duplicates_marked
if (!params.known_indels && step == 'mapping') bam_recalibrated = bam_duplicates_marked
if (!params.known_indels && step in ['mapping', 'preparerecalibration']) bam_recalibrated = bam_duplicates_marked

// When starting with variant calling, Channel bam_recalibrated is inputSample
if (step == 'variantcalling') bam_recalibrated = inputSample
Expand Down