Merge pull request #279 from MaxUlysse/fix_267

Fix 267
nf-core · Sep 2, 2020 · 7443459 · 7443459
2 parents 7b9a46d + 6db85c1
commit 7443459
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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
 

diff --git a/main.nf b/main.nf
@@ -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