Avoiding clashes of config of FILTERVARIANTTRANCHES in different subworkflows

.github/workflows/ci.yml

@@ -272,7 +272,7 @@ jobs:
           nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
           SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
           SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
-          SENTIEON_AUTH_DATA=$(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+          SENTIEON_AUTH_DATA=$(python3 bin/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
           SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
           nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
 

CHANGELOG.md

@@ -28,6 +28,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1287](https://github.com/nf-core/sarek/pull/1287) - Adding label `process_single` to local modules
 - [#1298](https://github.com/nf-core/sarek/pull/1298) - Fix annotation cache usage
 - [#1301](https://github.com/nf-core/sarek/pull/1301) - Fix nf-prov usage
+- [#1315](https://github.com/nf-core/sarek/pull/1315) - Avoid clash of configs of `FILTERVARIANTTRANCHES` in the Sentieon-Haplotyper and GATK-Haplotypecaller subworkflows
 
 ### Removed
 

conf/modules/haplotypecaller.config

@@ -43,7 +43,7 @@ process {
         ]
     }
 
-    withName: 'FILTERVARIANTTRANCHES' {
+    withName: '.*:VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES' {
         ext.prefix       = {"${meta.id}.haplotypecaller"}
         ext.args         = { "--info-key CNN_1D" }
         publishDir       = [

conf/modules/sentieon_dnascope.config

@@ -44,18 +44,6 @@ process {
         ]
     }
 
-    if (params.tools && params.tools.contains('sentieon_dnascope')) {
-        withName: '.*FILTERVARIANTTRANCHES' {
-            ext.prefix       = {"${meta.id}.dnascope"}
-            ext.args         = { "--info-key CNN_1D" }
-            publishDir       = [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/variant_calling/sentieon_dnascope/${meta.id}/"},
-                pattern: "*{vcf.gz,vcf.gz.tbi}"
-            ]
-        }
-    }
-
     withName: 'SENTIEON_DNAMODELAPPLY' {
         ext.prefix       = {"${meta.id}.dnascope.filtered"}
         publishDir       = [

conf/modules/sentieon_haplotyper.config

@@ -45,7 +45,7 @@ process {
     }
 
     if (params.tools && params.tools.contains('sentieon_haplotyper')) {
-        withName: '.*FILTERVARIANTTRANCHES' {
+        withName: '.*:SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK:FILTERVARIANTTRANCHES' {
             ext.prefix       = {"${meta.id}.haplotyper"}
             ext.args         = { "--info-key CNN_1D" }
             publishDir       = [

subworkflows/local/bam_variant_calling_germline_all/main.nf

@@ -2,20 +2,21 @@
 // GERMLINE VARIANT CALLING
 //
 
-include { BAM_JOINT_CALLING_GERMLINE_GATK         } from '../bam_joint_calling_germline_gatk/main'
-include { BAM_JOINT_CALLING_GERMLINE_SENTIEON     } from '../bam_joint_calling_germline_sentieon/main'
-include { BAM_VARIANT_CALLING_CNVKIT              } from '../bam_variant_calling_cnvkit/main'
-include { BAM_VARIANT_CALLING_DEEPVARIANT         } from '../bam_variant_calling_deepvariant/main'
-include { BAM_VARIANT_CALLING_FREEBAYES           } from '../bam_variant_calling_freebayes/main'
-include { BAM_VARIANT_CALLING_GERMLINE_MANTA      } from '../bam_variant_calling_germline_manta/main'
-include { BAM_VARIANT_CALLING_HAPLOTYPECALLER     } from '../bam_variant_calling_haplotypecaller/main'
-include { BAM_VARIANT_CALLING_SENTIEON_DNASCOPE   } from '../bam_variant_calling_sentieon_dnascope/main'
-include { BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER } from '../bam_variant_calling_sentieon_haplotyper/main'
-include { BAM_VARIANT_CALLING_MPILEUP             } from '../bam_variant_calling_mpileup/main'
-include { BAM_VARIANT_CALLING_SINGLE_STRELKA      } from '../bam_variant_calling_single_strelka/main'
-include { BAM_VARIANT_CALLING_SINGLE_TIDDIT       } from '../bam_variant_calling_single_tiddit/main'
-include { SENTIEON_DNAMODELAPPLY                  } from '../../../modules/nf-core/sentieon/dnamodelapply/main'
-include { VCF_VARIANT_FILTERING_GATK              } from '../vcf_variant_filtering_gatk/main'
+include { BAM_JOINT_CALLING_GERMLINE_GATK                                              } from '../bam_joint_calling_germline_gatk/main'
+include { BAM_JOINT_CALLING_GERMLINE_SENTIEON                                          } from '../bam_joint_calling_germline_sentieon/main'
+include { BAM_VARIANT_CALLING_CNVKIT                                                   } from '../bam_variant_calling_cnvkit/main'
+include { BAM_VARIANT_CALLING_DEEPVARIANT                                              } from '../bam_variant_calling_deepvariant/main'
+include { BAM_VARIANT_CALLING_FREEBAYES                                                } from '../bam_variant_calling_freebayes/main'
+include { BAM_VARIANT_CALLING_GERMLINE_MANTA                                           } from '../bam_variant_calling_germline_manta/main'
+include { BAM_VARIANT_CALLING_HAPLOTYPECALLER                                          } from '../bam_variant_calling_haplotypecaller/main'
+include { BAM_VARIANT_CALLING_SENTIEON_DNASCOPE                                        } from '../bam_variant_calling_sentieon_dnascope/main'
+include { BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER                                      } from '../bam_variant_calling_sentieon_haplotyper/main'
+include { BAM_VARIANT_CALLING_MPILEUP                                                  } from '../bam_variant_calling_mpileup/main'
+include { BAM_VARIANT_CALLING_SINGLE_STRELKA                                           } from '../bam_variant_calling_single_strelka/main'
+include { BAM_VARIANT_CALLING_SINGLE_TIDDIT                                            } from '../bam_variant_calling_single_tiddit/main'
+include { SENTIEON_DNAMODELAPPLY                                                       } from '../../../modules/nf-core/sentieon/dnamodelapply/main'
+include { VCF_VARIANT_FILTERING_GATK                                                   } from '../vcf_variant_filtering_gatk/main'
+include { VCF_VARIANT_FILTERING_GATK as SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK } from '../vcf_variant_filtering_gatk/main'
 
 
 
@@ -295,7 +296,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
             // If single sample track, check if filtering should be done
             if (!(skip_tools && skip_tools.split(',').contains('haplotyper_filter'))) {
 
-                VCF_VARIANT_FILTERING_GATK(
+                SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK(
                     vcf_sentieon_haplotyper.join(vcf_tbi_sentieon_haplotyper, failOnDuplicate: true, failOnMismatch: true),
                     fasta,
                     fasta_fai,
@@ -304,9 +305,9 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
                     known_sites_indels.concat(known_sites_snps).flatten().unique().collect(),
                     known_sites_indels_tbi.concat(known_sites_snps_tbi).flatten().unique().collect())
 
-                vcf_sentieon_haplotyper = VCF_VARIANT_FILTERING_GATK.out.filtered_vcf
+                vcf_sentieon_haplotyper = SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK.out.filtered_vcf
 
-                versions = versions.mix(VCF_VARIANT_FILTERING_GATK.out.versions)
+                versions = versions.mix(SENTIEON_HAPLOTYPER_VCF_VARIANT_FILTERING_GATK.out.versions)
             }
         }
     }

tests/test_sentieon_haplotyper.yml

@@ -145,3 +145,47 @@
     - path: results/variant_calling/sentieon_haplotyper/test/test.haplotyper.unfiltered.vcf.gz.tbi
     - path: results/haplotyper
       should_exist: false
+- name: Run variant calling on germline sample with sentieons haplotyper and gatk haplotypecaller
+  command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller,sentieon_haplotyper --step variant_calling --outdir results
+  tags:
+    - germline
+    - sentieon/haplotyper
+    - variant_calling
+  files:
+    - path: results/csv/variantcalled.csv
+      md5sum: caa9932235cf993fca208943d2e58041
+    - path: results/multiqc
+    - path: results/preprocessing/converted/test/test.converted.cram
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/converted/test/test.converted.cram.crai
+    # binary changes md5sums on reruns
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+      should_exist: false
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+      should_exist: false
+    - path: results/reports/bcftools/sentieon_haplotyper/test/test.haplotyper.filtered.bcftools_stats.txt
+      md5sum: 66be03d4e6535175514f54a1a031d49f
+    - path: results/reports/vcftools/sentieon_haplotyper/test/test.haplotyper.filtered.FILTER.summary
+      md5sum: d501a93356f3c91c743f51104e24514a
+    - path: results/reports/vcftools/sentieon_haplotyper/test/test.haplotyper.filtered.TsTv.count
+      md5sum: 89562fef808b5c3db629682d36fd86fc
+    - path: results/reports/vcftools/sentieon_haplotyper/test/test.haplotyper.filtered.TsTv.qual
+      # changes md5sum on reruns. This is somewhat unexpected, but might to tiny variation in very small numbers in the qual-files.
+    - path: results/variant_calling/sentieon_haplotyper/test/test.haplotyper.filtered.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_haplotyper/test/test.haplotyper.filtered.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_haplotyper/test/test.haplotyper.unfiltered.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/sentieon_haplotyper/test/test.haplotyper.unfiltered.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz
+    # binary changes md5sums on reruns
+    - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz.tbi
+    # binary changes md5sums on reruns
+    - path: results/haplotyper
+      should_exist: false