Merge pull request #870 from maxulysse/dev_ultima

fix bam output for haplotypecaller

Author: maxulysse

CHANGELOG.md

@@ -17,6 +17,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [#870](https://github.com/nf-core/sarek/pull/870) - Fix output for locally realigned reads from haplotypecaller
+
 ### Deprecated
 
 ### Removed

conf/modules/haplotypecaller.config

@@ -119,7 +119,7 @@ process {
         ]
     }
 
-    if (!(params.tools && params.tools.split(',').contains('haplotypecaller'))) {
+    if (params.tools && params.tools.split(',').contains('haplotypecaller')) {
         withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_HAPLOTYPECALLER:BAM_MERGE_INDEX_SAMTOOLS:(MERGE_BAM|INDEX_MERGE_BAM)' {
             ext.prefix       = { "${meta.id}.realigned" }
             publishDir       = [