From 4e30625cb70aec796a69502775da5f4ae6e2af41 Mon Sep 17 00:00:00 2001
From: SusiJo <susanne.jodoin@gmx.de>
Date: Wed, 13 Jul 2022 10:49:29 +0000
Subject: [PATCH] update outputs varcallers + ci tests

---
 conf/modules.config           |  76 +++++----
 tests/test_tools.yml          | 299 ++++++++++++++++++----------------
 tests/test_tools_manually.yml |  24 +--
 workflows/sarek.nf            |   6 +-
 4 files changed, 216 insertions(+), 189 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 7a85abdcc5..39986ca2f6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -514,6 +514,7 @@ process{
 
     // DEEPVARIANT
     withName: 'MERGE_DEEPVARIANT_.*' {
+        ext.prefix       = {"${meta.id}.deepvariant"}
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/deepvariant" },
@@ -521,10 +522,10 @@ process{
         ]
     }
     withName: 'MERGE_DEEPVARIANT_GVCF' {
-        ext.prefix       = {"${meta.id}.g"}
+        ext.prefix       = {"${meta.id}.deepvariant.g"}
     }
     withName: 'DEEPVARIANT' {
-        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}_${intervals.simpleName}" }
+        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.simpleName}" }
         ext.args         = { params.wes ?  "--model_type WES" : "--model_type WGS" }
         ext.when         = { params.tools && params.tools.contains('deepvariant') }
         publishDir       = [
@@ -535,6 +536,7 @@ process{
         ]
     }
     withName : 'TABIX_VC_DEEPVARIANT_.*' {
+        ext.prefix       = {"${meta.id}.deepvariant"}
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/deepvariant" },
@@ -544,6 +546,7 @@ process{
 
     // FREEBAYES
     withName: 'MERGE_FREEBAYES' {
+        ext.prefix       = { "${meta.id}.freebayes" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/freebayes" },
@@ -551,8 +554,8 @@ process{
         ]
     }
     withName: 'FREEBAYES' {
-        //To make sure no naming conflicts ensue with module BCFTOOLS_SORT & the naming being correct in the output folder
-        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${meta.id}_${target_bed.simpleName}.freebayes" }
+        //To make sure no naming conflicts ensure with module BCFTOOLS_SORT & the naming being correct in the output folder
+        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.simpleName}" }
         ext.args         = '--min-alternate-fraction 0.1 --min-mapping-quality 1'
         ext.when         = { params.tools && params.tools.contains('freebayes') }
         publishDir       = [
@@ -561,7 +564,7 @@ process{
     }
 
     withName: 'BCFTOOLS_SORT' {
-        ext.prefix       = { "${vcf.baseName.minus(".freebayes.vcf")}" }
+        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${vcf.minus("vcf")}.sort" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/" },
@@ -580,7 +583,7 @@ process{
 
     // HAPLOTYPECALLER
     withName: 'MERGE_HAPLOTYPECALLER.*' {
-        ext.prefix       = { params.joint_germline ? "${meta.id}.g" : "${meta.id}" }
+        ext.prefix       = { params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/haplotypecaller" },
@@ -590,7 +593,7 @@ process{
 
     withName: 'HAPLOTYPECALLER' {
         ext.args         = { params.joint_germline ? "-ERC GVCF" : "" }
-        ext.prefix       = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.g" : "${meta.id}" ) : ( params.joint_germline ? "${meta.id}_${intervals.simpleName}.g" :"${meta.id}_${intervals.simpleName}" ) }
+        ext.prefix       = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) }
         ext.when         = { params.tools && params.tools.contains('haplotypecaller') }
         publishDir       = [
             mode: params.publish_dir_mode,
@@ -605,6 +608,7 @@ process{
         ]
     }
     withName: 'FILTERVARIANTTRANCHES' {
+        ext.prefix       = {"${meta.id}.haplotypecaller"}
         ext.args         = { "--info-key CNN_1D" }
         publishDir       = [
             mode: params.publish_dir_mode,
@@ -614,6 +618,7 @@ process{
     }
 
     withName: 'GENOTYPEGVCFS' {
+        ext.prefix       = {"${meta.id}.haplotypecaller"}
         ext.when         = { params.tools && params.tools.contains('haplotypecaller') && params.joint_germline}
         publishDir       = [
             mode: params.publish_dir_mode,
@@ -631,16 +636,16 @@ process{
         ]
     }
     withName: 'MERGE_MANTA_DIPLOID' {
-        ext.prefix       = {"${meta.id}.diploid_sv"}
+        ext.prefix       = {"${meta.id}.manta.diploid_sv"}
     }
     withName: 'MERGE_MANTA_SMALL_INDELS' {
-        ext.prefix       = {"${meta.id}.candidate_small_indels"}
+        ext.prefix       = {"${meta.id}.manta.candidate_small_indels"}
     }
     withName: 'MERGE_MANTA_SV' {
-        ext.prefix       = {"${meta.id}.candidate_sv"}
+        ext.prefix       = {"${meta.id}.manta.candidate_sv"}
     }
     withName: 'MANTA.*' {
-        ext.prefix       = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${target_bed.simpleName}" }
+        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.manta" : "${meta.id}.manta.${target_bed.simpleName}" }
         ext.args         = { params.wes ? "--exome" : "" }
         ext.when         = { params.tools && params.tools.contains('manta') }
         publishDir       = [
@@ -660,13 +665,13 @@ process{
         ]
     }
     withName: 'MERGE_STRELKA' {
-        ext.prefix       = {"${meta.id}.variants"}
+        ext.prefix       = {"${meta.id}.strelka.variants"}
     }
     withName: 'MERGE_STRELKA_GENOME' {
-        ext.prefix       = {"${meta.id}.genome"}
+        ext.prefix       = {"${meta.id}.strelka.genome"}
     }
     withName: 'STRELKA_.*' {
-        ext.prefix       = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${target_bed.simpleName}" }
+        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.strelka" : "${meta.id}.strelka.${target_bed.simpleName}" }
         ext.args         = { params.wes ? "--exome" : "" }
         ext.when         = { params.tools && params.tools.contains('strelka') }
         publishDir       = [
@@ -681,6 +686,7 @@ process{
     withName: 'TIDDIT_SV' {
         ext.when         = { params.tools && params.tools.contains('tiddit') }
         ext.args         = { bwa_index ? "" : "--skip_assembly" }
+        ext.prefix       = { "${meta.id}.tiddit" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
@@ -688,7 +694,7 @@ process{
         ]
     }
     withName : 'TABIX_BGZIP_TIDDIT_SV' {
-        ext.prefix       = { "${meta.id}.vcf" }
+        ext.prefix       = { "${meta.id}.tiddit.vcf" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
@@ -825,13 +831,14 @@ process{
 
     //MANTA
     withName: 'MERGE_MANTA_TUMOR' {
-        ext.prefix       = {"${meta.id}.tumor_sv"}
+        ext.prefix       = {"${meta.id}.manta.tumor_sv"}
     }
 
     //MUTECT2
     withName: 'CALCULATECONTAMINATION' {
-        ext.args         = { "-tumor-segmentation ${meta.id}.segmentation.table" }
-        publishDir        = [
+        ext.prefix       = { "${meta.id}.mutect2" }
+        ext.args         = { "-tumor-segmentation ${meta.id}.mutect2.segmentation.table" }
+        publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.id}/mutect2/${filename}" }
@@ -839,6 +846,7 @@ process{
     }
 
     withName: 'MERGE_MUTECT2.*' {
+        ext.prefix       = { "${meta.id}.mutect2" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
@@ -847,7 +855,7 @@ process{
     }
 
     withName: 'FILTERMUTECTCALLS.*'{
-        ext.prefix       = {"${meta.id}.filtered"}
+        ext.prefix       = {"${meta.id}.mutect2.filtered"}
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
@@ -856,6 +864,7 @@ process{
     }
 
     withName: 'GATHERPILEUPSUMMARIES' {
+        ext.prefix       = { "${meta.id}.mutect2" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
@@ -864,6 +873,7 @@ process{
     }
 
     withName: 'GATHERPILEUPSUMMARIES_.*' {
+        ext.prefix       = { "${meta.id}.mutect2" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" },
@@ -872,7 +882,7 @@ process{
     }
 
     withName: 'GETPILEUPSUMMARIES.*' {
-        ext.prefix       = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${intervals.simpleName}" }
+        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
         publishDir        = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
@@ -882,6 +892,7 @@ process{
     }
 
     withName: 'GETPILEUPSUMMARIES_.*' {
+        ext.prefix        = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
         publishDir        = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/" },
@@ -891,7 +902,7 @@ process{
     }
 
     withName: 'LEARNREADORIENTATIONMODEL'{
-        ext.prefix       = { "${meta.id}.artifactprior" }
+        ext.prefix       = { "${meta.id}.mutect2.artifactprior" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
@@ -900,7 +911,7 @@ process{
     }
 
     withName: 'MERGEMUTECTSTATS' {
-        ext.prefix       = { "${meta.id}" }
+        ext.prefix       = { "${meta.id}.mutect2" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
@@ -909,7 +920,7 @@ process{
     }
 
     withName: 'MUTECT2'{
-        ext.prefix       = { meta.num_intervals <= 1 ? meta.id : "${meta.id}_${intervals.simpleName}" }
+        ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
         ext.when         = { params.tools && params.tools.contains('mutect2') }
         ext.args         = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" : "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" }
         publishDir       = [
@@ -1042,7 +1053,7 @@ process{
 
     //MANTA
     withName: 'MERGE_MANTA_SOMATIC' {
-        ext.prefix       = {"${meta.id}.somatic_sv"}
+        ext.prefix       = {"${meta.id}.manta.somatic_sv"}
     }
 
     //MUTECT2
@@ -1065,23 +1076,24 @@ process{
 
     //STRELKA
     withName: 'MERGE_STRELKA_INDELS' {
-        ext.prefix       = {"${meta.id}.somatic_indels"}
+        ext.prefix       = {"${meta.id}.strelka.somatic_indels"}
     }
     withName: 'MERGE_STRELKA_SNVS' {
-        ext.prefix       = {"${meta.id}.somatic_snvs"}
+        ext.prefix       = {"${meta.id}.strelka.somatic_snvs"}
     }
 
     //TIDDIT
     withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' {
-        ext.prefix       = {"${meta.id}.normal.vcf"}
+        ext.prefix       = {"${meta.id}.tiddit.normal.vcf"}
     }
 
     withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:RUN_TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' {
-        ext.prefix       = {"${meta.id}.tumor.vcf"}
+        ext.prefix       = {"${meta.id}.tiddit.tumor.vcf"}
     }
 
     //SVDB
     withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:SVDB_MERGE' {
+        ext.prefix       = { "${meta.id}.tiddit" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/tiddit" },
@@ -1092,20 +1104,20 @@ process{
     // VCF QC
     withName: 'BCFTOOLS_STATS'{
         ext.when         = { !(params.skip_tools && params.skip_tools.contains('bcftools')) }
-        ext.prefix       = { "${meta.variantcaller}.${vcf.baseName.minus(".vcf")}" }
+        ext.prefix       = { "${vcf.baseName.minus(".vcf")}" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/bcftools" },
+            path: { "${params.outdir}/reports/bcftools/${meta.id}/${meta.variantcaller}/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: 'VCFTOOLS_.*'{
         ext.when         = { !(params.skip_tools && params.skip_tools.contains('vcftools')) }
-        ext.prefix       = { "${meta.variantcaller}.${variant_file.baseName.minus(".vcf")}" }
+        ext.prefix       = { "${variant_file.baseName.minus(".vcf")}" }
         publishDir       = [
             mode: params.publish_dir_mode,
-            path: { "${params.outdir}/reports/vcftools" },
+            path: { "${params.outdir}/reports/vcftools/${meta.id}/${meta.variantcaller}/" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
diff --git a/tests/test_tools.yml b/tests/test_tools.yml
index 6dd0e63c25..5412bf8e62 100644
--- a/tests/test_tools.yml
+++ b/tests/test_tools.yml
@@ -151,10 +151,10 @@
     - germline
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/deepvariant/sample1.g.vcf.gz
-    - path: results/variant_calling/sample1/deepvariant/sample1.g.vcf.gz.tbi
-    - path: results/variant_calling/sample1/deepvariant/sample1.vcf.gz
-    - path: results/variant_calling/sample1/deepvariant/sample1.vcf.gz.tbi
+    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.g.vcf.gz
+    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.g.vcf.gz.tbi
+    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.vcf.gz
+    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on germline sample with deepvariant without intervals
@@ -165,10 +165,10 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/deepvariant/sample1.g.vcf.gz
-    - path: results/variant_calling/sample1/deepvariant/sample1.g.vcf.gz.tbi
-    - path: results/variant_calling/sample1/deepvariant/sample1.vcf.gz
-    - path: results/variant_calling/sample1/deepvariant/sample1.vcf.gz.tbi
+    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.g.vcf.gz
+    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.g.vcf.gz.tbi
+    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.vcf.gz
+    - path: results/variant_calling/sample1/deepvariant/sample1.deepvariant.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on germline sample with freebayes
@@ -178,8 +178,8 @@
     - germline
     - variant_calling
   files:
-    - path: results/variant_calling/test/freebayes/test.vcf.gz
-    - path: results/variant_calling/test/freebayes/test.vcf.gz.tbi
+    - path: results/variant_calling/test/freebayes/test.freebayes.vcf.gz
+    - path: results/variant_calling/test/freebayes/test.freebayes.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on germline sample with freebayes without intervals
@@ -190,8 +190,8 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/test/freebayes/test.vcf.gz
-    - path: results/variant_calling/test/freebayes/test.vcf.gz.tbi
+    - path: results/variant_calling/test/freebayes/test.freebayes.vcf.gz
+    - path: results/variant_calling/test/freebayes/test.freebayes.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with freebayes
@@ -201,8 +201,8 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.vcf.gz
-    - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.vcf.gz.tbi
+    - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.freebayes.vcf.gz
+    - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.freebayes.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with freebayes without intervals
@@ -213,8 +213,8 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.vcf.gz
-    - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.vcf.gz.tbi
+    - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.freebayes.vcf.gz
+    - path: results/variant_calling/test2_vs_test/freebayes/test2_vs_test.freebayes.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 # - name: Run variant calling on tumor_only sample with freebayes
@@ -224,8 +224,8 @@
 #     - tumor_only
 #     - variant_calling
 #   files:
-#     - path: results/variant_calling/sample2/freebayes/sample2.vcf.gz
-#     - path: results/variant_calling/sample2/freebayes/sample2.vcf.gz.tbi
+#     - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz
+#     - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz.tbi
 
 # - name: Run variant calling on tumor_only sample with freebayes without intervals
 #   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools freebayes --no_intervals
@@ -235,8 +235,8 @@
 #     - tumor_only
 #     - variant_calling
 #   files:
-#     - path: results/variant_calling/sample2/freebayes/sample2.vcf.gz
-#     - path: results/variant_calling/sample2/freebayes/sample2.vcf.gz.tbi
+#     - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz
+#     - path: results/variant_calling/sample2/freebayes/sample2.freebayes.vcf.gz.tbi
 
 - name: Run variant calling on germline sample with haplotypecaller
   command: nextflow run main.nf -profile test,targeted,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller  -c ./tests/nextflow.config --step variant_calling
@@ -245,11 +245,15 @@
     - haplotypecaller
     - variant_calling
   files:
-    - path: results/variant_calling/test/haplotypecaller/test.vcf.gz
-    - path: results/variant_calling/test/haplotypecaller/test.vcf.gz.tbi
-    - path: results/variant_calling/test/haplotypecaller/test.filtered.vcf.gz
-    - path: results/variant_calling/test/haplotypecaller/test.filtered.vcf.gz.tbi
+    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.vcf.gz
+    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.vcf.gz.tbi
+    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz
+    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
+    - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.vcf.gz
+    - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.vcf.gz.tbi
+    - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz
+    - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi
 
 - name: Run variant calling on germline sample with haplotypecaller without intervals
   command: nextflow run main.nf -profile test,docker --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller  -c ./tests/nextflow.config --step variant_calling --no_intervals
@@ -259,11 +263,15 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/test/haplotypecaller/test.vcf.gz
-    - path: results/variant_calling/test/haplotypecaller/test.vcf.gz.tbi
-    - path: results/variant_calling/test/haplotypecaller/test.filtered.vcf.gz
-    - path: results/variant_calling/test/haplotypecaller/test.filtered.vcf.gz.tbi
+    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.vcf.gz
+    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.vcf.gz.tbi
+    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz
+    - path: results/variant_calling/test/haplotypecaller/test.haplotypecaller.filtered.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
+    - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.vcf.gz
+    - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.vcf.gz.tbi
+    - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz
+    - path: results/variant_calling/test/haplotypecaller/test1.haplotypecaller.filtered.vcf.gz.tbi
 
 # - name: Run joint germline variant calling with haplotypecaller
 #   command: nextflow run main.nf -profile test,tools_germline,docker --tools haplotypecaller --joint_germline -c ./tests/nextflow.config
@@ -273,10 +281,10 @@
 #     - haplotypecaller
 #     - variant_calling
 #   files:
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.g.vcf.gz
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.g.vcf.gz.tbi
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.vcf.gz
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.vcf.gz.tbi
+#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.g.vcf.gz
+#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.g.vcf.gz.tbi
+#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.vcf.gz
+#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.vcf.gz.tbi
 #     - path: results/csv/variantcalled.csv
 
 # - name: Run joint germline variant calling with haplotypecaller without intervals
@@ -288,10 +296,10 @@
 #     - no_intervals
 #     - variant_calling
 #   files:
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.g.vcf.gz
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.g.vcf.gz.tbi
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.vcf.gz
-#     - path: results/variant_calling/sample1/haplotypecaller/sample1.vcf.gz.tbi
+#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.g.vcf.gz
+#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.g.vcf.gz.tbi
+#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.vcf.gz
+#     - path: results/variant_calling/sample1/haplotypecaller/sample1.haplotypecaller.vcf.gz.tbi
 #     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on germline sample with manta
@@ -301,8 +309,8 @@
     - manta
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample1/manta/sample1.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/sample1/manta/sample1.manta.diploid_sv.vcf.gz.tbi
 
 - name: Run variant calling on germline sample with manta without intervals
   command: nextflow run main.nf -profile test,tools_germline,docker --tools manta --no_intervals
@@ -312,8 +320,8 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample1/manta/sample1.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample1/manta/sample1.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/sample1/manta/sample1.manta.diploid_sv.vcf.gz.tbi
 
 - name: Run variant calling on tumor_only sample with manta
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools manta
@@ -322,8 +330,8 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz
-    - path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample2/manta/sample2.manta.tumor_sv.vcf.gz
+    - path: results/variant_calling/sample2/manta/sample2.manta.tumor_sv.vcf.gz.tbi
 
 - name: Run variant calling on tumor_only sample with manta without intervals
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools manta --no_intervals
@@ -333,8 +341,8 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz
-    - path: results/variant_calling/sample2/manta/sample2.tumor_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample2/manta/sample2.manta.tumor_sv.vcf.gz
+    - path: results/variant_calling/sample2/manta/sample2.manta.tumor_sv.vcf.gz.tbi
 
 - name: Run variant calling on somatic sample with manta
   command: nextflow run main.nf -profile test,tools_somatic,docker --tools manta
@@ -343,12 +351,12 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
 
 - name: Run variant calling on somatic sample with manta without intervals
   command: nextflow run main.nf -profile test,tools_somatic,docker --tools manta --no_intervals
@@ -358,12 +366,12 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample3/manta/sample3.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.diploid_sv.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.somatic_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
 
 - name: Run variant calling on tumor_only sample to test mpileup
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools mpileup
@@ -406,16 +414,16 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/mutect2/sample2.vcf.gz
-    - path: results/variant_calling/sample2/mutect2/sample2.vcf.gz.tbi
-    - path: results/variant_calling/sample2/mutect2/sample2.vcf.gz.stats
-    - path: results/variant_calling/sample2/mutect2/sample2.contamination.table
-    - path: results/variant_calling/sample2/mutect2/sample2.segmentation.table
-    - path: results/variant_calling/sample2/mutect2/sample2.artifactprior.tar.gz
-    - path: results/variant_calling/sample2/mutect2/sample2.pileupsummaries.table
-    - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz
-    - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz.tbi
-    - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz.filteringStats.tsv
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz.tbi
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz.stats
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.contamination.table
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.segmentation.table
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.artifactprior.tar.gz
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.pileupsummaries.table
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz.tbi
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz.filteringStats.tsv
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on tumoronly sample with mutect2 without intervals
@@ -426,16 +434,17 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/mutect2/sample2.vcf.gz
-    - path: results/variant_calling/sample2/mutect2/sample2.vcf.gz.tbi
-    - path: results/variant_calling/sample2/mutect2/sample2.vcf.gz.stats
-    - path: results/variant_calling/sample2/mutect2/sample2.contamination.table
-    - path: results/variant_calling/sample2/mutect2/sample2.segmentation.table
-    - path: results/variant_calling/sample2/mutect2/sample2.artifactprior.tar.gz
-    - path: results/variant_calling/sample2/mutect2/sample2.pileupsummaries.table
-    - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz
-    - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz.tbi
-    - path: results/variant_calling/sample2/mutect2/sample2.filtered.vcf.gz.filteringStats.tsv
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.pileups.table
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz.tbi
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.vcf.gz.stats
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.contamination.table
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.segmentation.table
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.artifactprior.tar.gz
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.pileupsummaries.table
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz.tbi
+    - path: results/variant_calling/sample2/mutect2/sample2.mutect2.filtered.vcf.gz.filteringStats.tsv
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with mutect2
@@ -446,17 +455,17 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz.stats
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.contamination.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.segmentation.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.pileupsummaries.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.pileupsummaries.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.artifactprior.tar.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz.filteringStats.tsv
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz.stats
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.contamination.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.segmentation.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.mutect2.pileupsummaries.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.mutect2.pileupsummaries.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.artifactprior.tar.gz
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz.filteringStats.tsv
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with msisensor-pro
@@ -478,10 +487,10 @@
     - strelka
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz
-    - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz
-    - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz.tbi
+    - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz
+    - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz
+    - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on germline sample with strelka without intervals
@@ -492,10 +501,10 @@
     - no_intervals
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz
-    - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz
-    - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz.tbi
+    - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz
+    - path: results/variant_calling/sample1/strelka/sample1.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz
+    - path: results/variant_calling/sample1/strelka/sample1.strelka.genome.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on tumoronly sample with strelka
@@ -505,10 +514,10 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz
-    - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz
-    - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz.tbi
+    - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz
+    - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz
+    - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on tumoronly sample with strelka without intervals
@@ -519,10 +528,10 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz
-    - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz
-    - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz.tbi
+    - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz
+    - path: results/variant_calling/sample2/strelka/sample2.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz
+    - path: results/variant_calling/sample2/strelka/sample2.strelka.genome.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with strelka
@@ -532,14 +541,14 @@
     - strelka
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi
+    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz
+    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz
+    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with strelka without intervals
@@ -550,14 +559,14 @@
     - strelka
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi
+    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz
+    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz
+    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with strelka & manta (StrelkaBP)
@@ -585,14 +594,20 @@
     - strelkabp
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi
-    - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz
-    - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi
+    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/sample3/manta/sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz
+    - path: results/variant_calling/sample3/strelka/sample3.strelka.genome.vcf.gz.tbi
+    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz
+    - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/manta/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi
     - path: results/csv/variantcalled.csv
 
 - name: Run variant calling on somatic sample with tiddit
@@ -602,15 +617,15 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample3/tiddit/sample3.ploidies.tab
-    - path: results/variant_calling/sample3/tiddit/sample3.vcf.gz
-    - path: results/variant_calling/sample3/tiddit/sample3.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.normal.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.normal.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tumor.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tumor.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3_sv_merge.vcf
-    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.ploidies.tab
+    - path: results/variant_calling/sample3/tiddit/sample3.tiddit.ploidies.tab
+    - path: results/variant_calling/sample3/tiddit/sample3.tiddit.vcf.gz
+    - path: results/variant_calling/sample3/tiddit/sample3.tiddit.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.normal.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.normal.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.tumor.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.tumor.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit_sv_merge.vcf
+    - path: results/variant_calling/sample4_vs_sample3/tiddit/sample4_vs_sample3.tiddit.ploidies.tab
 
 - name: Run variant calling on germline sample with tiddit
   command: nextflow run main.nf -profile test,tools_germline,docker --tools tiddit -c ./tests/nextflow.config
@@ -619,9 +634,9 @@
     - germline
     - variant_calling
   files:
-    - path: results/variant_calling/sample1/tiddit/sample1.ploidies.tab
-    - path: results/variant_calling/sample1/tiddit/sample1.vcf.gz
-    - path: results/variant_calling/sample1/tiddit/sample1.vcf.gz.tbi
+    - path: results/variant_calling/sample1/tiddit/sample1.tiddit.ploidies.tab
+    - path: results/variant_calling/sample1/tiddit/sample1.tiddit.vcf.gz
+    - path: results/variant_calling/sample1/tiddit/sample1.tiddit.vcf.gz.tbi
 
 - name: Run variant calling on tumor_only sample with tiddit
   command: nextflow run main.nf -profile test,tools_tumoronly,docker --tools tiddit -c ./tests/nextflow.config
@@ -630,6 +645,6 @@
     - tumor_only
     - variant_calling
   files:
-    - path: results/variant_calling/sample2/tiddit/sample2.ploidies.tab
-    - path: results/variant_calling/sample2/tiddit/sample2.vcf.gz
-    - path: results/variant_calling/sample2/tiddit/sample2.vcf.gz.tbi
+    - path: results/variant_calling/sample2/tiddit/sample2.tiddit.ploidies.tab
+    - path: results/variant_calling/sample2/tiddit/sample2.tiddit.vcf.gz
+    - path: results/variant_calling/sample2/tiddit/sample2.tiddit.vcf.gz.tbi
diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml
index 749d29c3ea..925b3ea3d5 100644
--- a/tests/test_tools_manually.yml
+++ b/tests/test_tools_manually.yml
@@ -32,15 +32,17 @@
     - somatic
     - variant_calling
   files:
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.vcf.gz.stats
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.contamination.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.segmentation.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.pileupsummaries.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.pileupsummaries.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.artifactprior.tar.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz.tbi
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.filtered.vcf.gz.filteringStats.tsv
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.mutect2.pileups.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.mutect2.pileups.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.vcf.gz.stats
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.contamination.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.segmentation.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample3.mutect2.pileupsummaries.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.mutect2.pileupsummaries.table
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.artifactprior.tar.gz
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz.tbi
+    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.mutect2.filtered.vcf.gz.filteringStats.tsv
     - path: results/csv/variantcalled.csv
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index 72c7b71685..63bfbcac6b 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -761,7 +761,7 @@ workflow SAREK {
             }.set{convert}
 
         //BAM files first must be converted to CRAM files since from this step on we base everything on CRAM format
-        BAMTOCRAM_VARIANTCALLING(convert.bam, fasta, fasta_fai)
+        SAMTOOLS_BAMTOCRAM_VARIANTCALLING(convert.bam, fasta, fasta_fai)
         ch_versions = ch_versions.mix(SAMTOOLS_BAMTOCRAM_VARIANTCALLING.out.versions)
 
         cram_variant_calling = Channel.empty().mix(SAMTOOLS_BAMTOCRAM_VARIANTCALLING.out.alignment_index, convert.cram)
@@ -912,6 +912,7 @@ workflow SAREK {
         vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.manta_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.strelka_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.tiddit_vcf)
+        vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.freebayes_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.mutect2_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.manta_vcf)
         vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.strelka_vcf)
@@ -923,7 +924,6 @@ workflow SAREK {
         ch_versions = ch_versions.mix(TUMOR_ONLY_VARIANT_CALLING.out.versions)
 
         //QC
-        vcf_to_annotate.dump(tag:'vcf_to_annotate')
         VCF_QC(vcf_to_annotate, intervals_bed_combined)
 
         ch_versions = ch_versions.mix(VCF_QC.out.versions)
@@ -976,8 +976,6 @@ workflow SAREK {
                                             ch_reports.collect()
                                             )
 
-        ch_multiqc_files.view()
-
         MULTIQC(ch_multiqc_files.collect(), ch_multiqc_config)
         multiqc_report = MULTIQC.out.report.toList()
     }