Merge pull request #1050 from amizeranschi/amizeranschi-issue-1025

Disable GATK filters when joint calling

CHANGELOG.md

@@ -70,6 +70,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1040](https://github.com/nf-core/sarek/pull/1040) - Fix dict channel issue due to [#1032](https://github.com/nf-core/sarek/pull/1032)
 - [#1043](https://github.com/nf-core/sarek/pull/1043) - Fix typo in the tags.yml files from [#978](https://github.com/nf-core/sarek/pull/978)
 - [#1048](https://github.com/nf-core/sarek/pull/1048) - Skip tool validation on annotation to fix [#949](https://github.com/nf-core/sarek/issues/949), check that bam is bam and cram is cram [#895](https://github.com/nf-core/sarek/issues/895)
+- [#1050](https://github.com/nf-core/sarek/pull/1050) - Disable GATK VCF filters when joint calling to fix [#1025](https://github.com/nf-core/sarek/issues/1025)
 
 ### Removed
 

subworkflows/local/bam_variant_calling_germline_all/main.nf

@@ -122,7 +122,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
             known_snps_vqsr,
             intervals,
             intervals_bed_combined_haplotypec,
-            (skip_tools && skip_tools.split(',').contains('haplotypecaller_filter')))
+            ((skip_tools && skip_tools.split(',').contains('haplotypecaller_filter') || joint_germline)))
 
         vcf_haplotypecaller = BAM_VARIANT_CALLING_HAPLOTYPECALLER.out.vcf
         versions = versions.mix(BAM_VARIANT_CALLING_HAPLOTYPECALLER.out.versions)