don't use freebayes for bcftools sort on joint germline

CHANGELOG.md

@@ -42,6 +42,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#727](https://github.com/nf-core/sarek/pull/727) - Allow `.list` interval files; remove `seconds` from GRCh38 file to allow `--nucleotides_per_second` to be used
 - [#728](https://github.com/nf-core/sarek/pull/728) - Circumvent issue with controlfreec and length file containing regions not in intervals file
 - [#729](https://github.com/nf-core/sarek/pull/729) - Trailing commas in `--tools`, `--skip_tools` and `--use_gatk_spark` now raise failure cf [#722](https://github.com/nf-core/sarek/issues/722)
+- [#741](https://github.com/nf-core/sarek/pull/741) - Fix prefix for `bcftools sort` for joint germline variant calling
 
 ### Deprecated
 

conf/modules.config

@@ -758,14 +758,21 @@ process{
     }
 
     withName: 'GATK4_GENOMICSDBIMPORT' {
-        ext.prefix       = { meta.num_intervals > 1 ? meta.intervals_name : "joint_interval" }
+        ext.prefix       = { meta.num_intervals > 1 ? "${meta.intervals_name}.joint" : "joint" }
         ext.when         = { params.tools && params.tools.split(',').contains('haplotypecaller') && params.joint_germline && !params.no_intervals}
     }
 
     withName: 'GATK4_GENOTYPEGVCFS' {
         ext.prefix       = { meta.num_intervals > 1 ? meta.intervals_name : "joint_germline" }
     }
 
+    withName: 'NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:BCFTOOLS_SORT' {
+        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.joint.sort" : "${vcf.minus("vcf.gz")}.sort" }
+        publishDir       = [
+            enabled: false
+        ]
+    }
+
     withName: 'MERGE_GENOTYPEGVCFS' {
         ext.prefix       = "joint_germline"
         publishDir       = [