diff --git a/CHANGELOG.md b/CHANGELOG.md
index 99b4f6d855..4fb2d08bec 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,12 +14,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [#859](https://github.com/nf-core/sarek/pull/859) - Back to dev
-- [#860](https://github.com/nf-core/sarek/pull/860) - replace local subworkflow with nf-core version - vcf_annotate_snpeff
-- [#865](https://github.com/nf-core/sarek/pull/865) - replace local subworkflow with nf-core version - vcf_annotate_ensemblvep
+- [#860](https://github.com/nf-core/sarek/pull/860) - Replace local subworkflow with nf-core version - vcf_annotate_snpeff
+- [#865](https://github.com/nf-core/sarek/pull/865) - Replace local subworkflow with nf-core version - vcf_annotate_ensemblvep
+- [#874](https://github.com/nf-core/sarek/pull/874) - Update all modules
 
 ### Fixed
 
 - [#870](https://github.com/nf-core/sarek/pull/870) - Fix output for locally realigned reads from haplotypecaller
+- [#874](https://github.com/nf-core/sarek/pull/874) - Remove `CITATION.cff`
 
 ### Deprecated
 
@@ -27,6 +29,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Dependencies
 
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `svdb`     | 2.6.1       | 2.8.1       |
+
 ## [3.1.1](https://github.com/nf-core/sarek/releases/tag/3.1.1) - Lilla Luleälven
 
 Lilla Luleälven river's main affluent is Rapaätno.
diff --git a/CITATION.cff b/CITATION.cff
deleted file mode 100644
index 017666c018..0000000000
--- a/CITATION.cff
+++ /dev/null
@@ -1,56 +0,0 @@
-cff-version: 1.2.0
-message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication"
-authors:
-  - family-names: Ewels
-    given-names: Philip
-  - family-names: Peltzer
-    given-names: Alexander
-  - family-names: Fillinger
-    given-names: Sven
-  - family-names: Patel
-    given-names: Harshil
-  - family-names: Alneberg
-    given-names: Johannes
-  - family-names: Wilm
-    given-names: Andreas
-  - family-names: Garcia
-    given-names: Maxime Ulysse
-  - family-names: Di Tommaso
-    given-names: Paolo
-  - family-names: Nahnsen
-    given-names: Sven
-title: "The nf-core framework for community-curated bioinformatics pipelines."
-version: 2.4.1
-doi: 10.1038/s41587-020-0439-x
-date-released: 2022-05-16
-url: https://github.com/nf-core/tools
-prefered-citation:
-  type: article
-  authors:
-    - family-names: Ewels
-      given-names: Philip
-    - family-names: Peltzer
-      given-names: Alexander
-    - family-names: Fillinger
-      given-names: Sven
-    - family-names: Patel
-      given-names: Harshil
-    - family-names: Alneberg
-      given-names: Johannes
-    - family-names: Wilm
-      given-names: Andreas
-    - family-names: Garcia
-      given-names: Maxime Ulysse
-    - family-names: Di Tommaso
-      given-names: Paolo
-    - family-names: Nahnsen
-      given-names: Sven
-  doi: 10.1038/s41587-020-0439-x
-  journal: nature biotechnology
-  start: 276
-  end: 278
-  title: "The nf-core framework for community-curated bioinformatics pipelines."
-  issue: 3
-  volume: 38
-  year: 2020
-  url: https://dx.doi.org/10.1038/s41587-020-0439-x
diff --git a/modules.json b/modules.json
index 05c489d2d3..85f891c49b 100644
--- a/modules.json
+++ b/modules.json
@@ -32,7 +32,7 @@
                     },
                     "bwa/mem": {
                         "branch": "master",
-                        "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
+                        "git_sha": "653588be2a4aadab487b530643dbc9baf7a485c4",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
@@ -42,7 +42,7 @@
                     },
                     "bwamem2/mem": {
                         "branch": "master",
-                        "git_sha": "cf5b9c30a2adacc581793afb79fae5f5b50bed01",
+                        "git_sha": "653588be2a4aadab487b530643dbc9baf7a485c4",
                         "installed_by": ["modules"]
                     },
                     "cat/cat": {
@@ -119,8 +119,8 @@
                     },
                     "ensemblvep": {
                         "branch": "master",
-                        "git_sha": "69f158610f25a3bff40b3eadfedd3ac67a3cfc23",
-                        "installed_by": ["modules", "vcf_annotate_ensemblvep"]
+                        "git_sha": "1ec0d59beb1e794a7a4a4351e15138ffa213aa20",
+                        "installed_by": ["vcf_annotate_ensemblvep", "modules"]
                     },
                     "fastp": {
                         "branch": "master",
@@ -129,7 +129,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "3dd73937b084b547f9272bc901e0f120a7913fd8",
+                        "git_sha": "810e8f2603ec38401d49a4aaed06f6d058745552",
                         "installed_by": ["modules"]
                     },
                     "fgbio/callmolecularconsensusreads": {
@@ -265,7 +265,7 @@
                     },
                     "gatk4/mergevcfs": {
                         "branch": "master",
-                        "git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67",
+                        "git_sha": "c25943553f62be5f907e3c12c42eaf0a1b40746d",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mutect2": {
@@ -381,7 +381,7 @@
                     },
                     "svdb/merge": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
+                        "git_sha": "4a8a2caf44b87734b41ea4c67f508c14f0745ee7",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {
diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf
index 7eb9d5c2cf..363d1f2e0e 100644
--- a/modules/nf-core/bwa/mem/main.nf
+++ b/modules/nf-core/bwa/mem/main.nf
@@ -25,7 +25,7 @@ process BWA_MEM {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def samtools_command = sort_bam ? 'sort' : 'view'
     """
-    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
+    INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
 
     bwa mem \\
         $args \\
diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf
index f8bad4b94a..84b99dfa02 100644
--- a/modules/nf-core/bwamem2/mem/main.nf
+++ b/modules/nf-core/bwamem2/mem/main.nf
@@ -25,7 +25,7 @@ process BWAMEM2_MEM {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def samtools_command = sort_bam ? 'sort' : 'view'
     """
-    INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
+    INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
 
     bwa-mem2 \\
         mem \\
diff --git a/modules/nf-core/ensemblvep/main.nf b/modules/nf-core/ensemblvep/main.nf
index 614852f367..a6049034e6 100644
--- a/modules/nf-core/ensemblvep/main.nf
+++ b/modules/nf-core/ensemblvep/main.nf
@@ -8,7 +8,7 @@ process ENSEMBLVEP {
         'quay.io/biocontainers/ensembl-vep:108.2--pl5321h4a94de4_0' }"
 
     input:
-    tuple val(meta), path(vcf, stageAs: "?/*")
+    tuple val(meta), path(vcf)
     val   genome
     val   species
     val   cache_version
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 3bebb2407a..47fd0e5843 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -21,9 +21,15 @@ process FASTQC {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    // Make list of old name and new name pairs to use for renaming in the bash while loop
+    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
+    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
     """
-    printf "%s\\n" $reads | while read f; do [[ \$f =~ ^${prefix}.* ]] || ln -s \$f ${prefix}_\$f ; done
-    fastqc $args --threads $task.cpus ${prefix}*
+    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
+    done
+    fastqc $args --threads $task.cpus $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/gatk4/mergevcfs/main.nf b/modules/nf-core/gatk4/mergevcfs/main.nf
index 0b065b5b55..08fb3969e3 100644
--- a/modules/nf-core/gatk4/mergevcfs/main.nf
+++ b/modules/nf-core/gatk4/mergevcfs/main.nf
@@ -9,7 +9,7 @@ process GATK4_MERGEVCFS {
 
     input:
     tuple val(meta), path(vcf)
-    path  dict
+    tuple val(meta2), path(dict)
 
     output:
     tuple val(meta), path('*.vcf.gz'), emit: vcf
diff --git a/modules/nf-core/gatk4/mergevcfs/meta.yml b/modules/nf-core/gatk4/mergevcfs/meta.yml
index 3ebce0b9e1..db8c4cb0bf 100644
--- a/modules/nf-core/gatk4/mergevcfs/meta.yml
+++ b/modules/nf-core/gatk4/mergevcfs/meta.yml
@@ -23,13 +23,16 @@ input:
       type: list
       description: Two or more VCF files
       pattern: "*.{vcf,vcf.gz}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome']
   - ref_dict:
       type: file
       description: Optional Sequence Dictionary as input
       pattern: "*.dict"
-  - use_ref_dict:
-      type: boolean
-      description: Specify whether or not to use a given reference dictionary
+
 output:
   - vcf:
       type: file
diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf
index 477dbb0d31..7dd926537f 100644
--- a/modules/nf-core/svdb/merge/main.nf
+++ b/modules/nf-core/svdb/merge/main.nf
@@ -1,10 +1,10 @@
 process SVDB_MERGE {
     tag "$meta.id"
     label 'process_medium'
-    conda (params.enable_conda ? "bioconda::svdb=2.6.1 bioconda::samtools=1.15.1" : null)
+    conda (params.enable_conda ? "bioconda::svdb=2.8.1 bioconda::samtools=1.16.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0':
-        'quay.io/biocontainers/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:af6f8534cd538a85ff43a2eae1b52b143e7abd05-0':
+        'quay.io/biocontainers/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:af6f8534cd538a85ff43a2eae1b52b143e7abd05-0' }"
 
     input:
     tuple val(meta), path(vcfs)
diff --git a/subworkflows/local/bam_joint_calling_germline_gatk/main.nf b/subworkflows/local/bam_joint_calling_germline_gatk/main.nf
index c930a1cc2d..f862f7bd07 100644
--- a/subworkflows/local/bam_joint_calling_germline_gatk/main.nf
+++ b/subworkflows/local/bam_joint_calling_germline_gatk/main.nf
@@ -1,15 +1,15 @@
 //
 // merge samples with genomicsdbimport, perform joint genotyping with genotypeGVCFS
-include { BCFTOOLS_SORT                                         } from '../../../modules/nf-core/bcftools/sort/main'
-include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_INDEL              } from '../../../modules/nf-core/gatk4/applyvqsr/main'
-include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_SNP                } from '../../../modules/nf-core/gatk4/applyvqsr/main'
-include { GATK4_GENOMICSDBIMPORT                                } from '../../../modules/nf-core/gatk4/genomicsdbimport/main'
-include { GATK4_GENOTYPEGVCFS                                   } from '../../../modules/nf-core/gatk4/genotypegvcfs/main'
-include { GATK4_MERGEVCFS as MERGE_GENOTYPEGVCFS                } from '../../../modules/nf-core/gatk4/mergevcfs/main'
-include { GATK4_MERGEVCFS as MERGE_VQSR                         } from '../../../modules/nf-core/gatk4/mergevcfs/main'
-include { GATK4_VARIANTRECALIBRATOR as VARIANTRECALIBRATOR_INDEL} from '../../../modules/nf-core/gatk4/variantrecalibrator/main'
-include { GATK4_VARIANTRECALIBRATOR as VARIANTRECALIBRATOR_SNP  } from '../../../modules/nf-core/gatk4/variantrecalibrator/main'
-include { TABIX_TABIX as TABIX                                  } from '../../../modules/nf-core/tabix/tabix/main'
+include { BCFTOOLS_SORT                                          } from '../../../modules/nf-core/bcftools/sort/main'
+include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_INDEL               } from '../../../modules/nf-core/gatk4/applyvqsr/main'
+include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_SNP                 } from '../../../modules/nf-core/gatk4/applyvqsr/main'
+include { GATK4_GENOMICSDBIMPORT                                 } from '../../../modules/nf-core/gatk4/genomicsdbimport/main'
+include { GATK4_GENOTYPEGVCFS                                    } from '../../../modules/nf-core/gatk4/genotypegvcfs/main'
+include { GATK4_MERGEVCFS as MERGE_GENOTYPEGVCFS                 } from '../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_MERGEVCFS as MERGE_VQSR                          } from '../../../modules/nf-core/gatk4/mergevcfs/main'
+include { GATK4_VARIANTRECALIBRATOR as VARIANTRECALIBRATOR_INDEL } from '../../../modules/nf-core/gatk4/variantrecalibrator/main'
+include { GATK4_VARIANTRECALIBRATOR as VARIANTRECALIBRATOR_SNP   } from '../../../modules/nf-core/gatk4/variantrecalibrator/main'
+include { TABIX_TABIX as TABIX                                   } from '../../../modules/nf-core/tabix/tabix/main'
 
 workflow BAM_JOINT_CALLING_GERMLINE_GATK {
     take:
@@ -72,13 +72,13 @@ workflow BAM_JOINT_CALLING_GERMLINE_GATK {
         no_intervals: it[0].num_intervals <= 1
     }
 
-    vcfs_sorted_input_no_intervals =  vcfs_sorted_input.no_intervals.map{ meta , vcf ->
-
-                            [[  id:             "joint_variant_calling",
-                                num_intervals:  meta.num_intervals,
-                                patient:        "all_samples",
-                                variantcaller:  "haplotypecaller"
-                            ] , vcf ]
+    vcfs_sorted_input_no_intervals =  vcfs_sorted_input.no_intervals.map{ meta, vcf ->
+        [[
+            id:             "joint_variant_calling",
+            num_intervals:  meta.num_intervals,
+            patient:        "all_samples",
+            variantcaller:  "haplotypecaller"
+        ], vcf ]
     }
 
     // Index vcf files if no scatter/gather by intervals
@@ -86,17 +86,15 @@ workflow BAM_JOINT_CALLING_GERMLINE_GATK {
 
     //Merge scatter/gather vcfs & index
     //Rework meta for variantscalled.csv and annotation tools
-    MERGE_GENOTYPEGVCFS(vcfs_sorted_input.intervals.map{meta, vcf ->
-                                [
-                                        [
-                                            id: "joint_variant_calling",
-                                            num_intervals: meta.num_intervals,
-                                            patient: "all_samples",
-                                            variantcaller: "haplotypecaller",
-                                        ],
-                                vcf]
-                            }.groupTuple()
-                            ,dict)
+    MERGE_GENOTYPEGVCFS(vcfs_sorted_input.intervals.map{ meta, vcf ->
+            [[
+                id:             "joint_variant_calling",
+                num_intervals:  meta.num_intervals,
+                patient:        "all_samples",
+                variantcaller:  "haplotypecaller"
+            ], vcf ]
+        }.groupTuple(),
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     vqsr_input = Channel.empty().mix(
         MERGE_GENOTYPEGVCFS.out.vcf.join(MERGE_GENOTYPEGVCFS.out.tbi),
@@ -134,46 +132,45 @@ workflow BAM_JOINT_CALLING_GERMLINE_GATK {
 
     //Join results of variant recalibration into a single channel tuple
     //Rework meta for variantscalled.csv and annotation tools
-    vqsr_input_snp   = vqsr_input.join( VARIANTRECALIBRATOR_SNP.out.recal)
-                                .join( VARIANTRECALIBRATOR_SNP.out.idx)
-                                .join( VARIANTRECALIBRATOR_SNP.out.tranches)
-                                .map{ meta, vcf, tbi, recal, index, tranche ->
-
-                                            new_meta = [
-                                                        id:             "recalibrated_joint_variant_calling",
-                                                        num_intervals:  meta.num_intervals,
-                                                        patient:        "all_samples",
-                                                        variantcaller:  "haplotypecaller",
-                                                    ]
-
-                                            [new_meta, vcf, tbi, recal, index, tranche]
-                                        }
+    vqsr_input_snp   = vqsr_input.join(VARIANTRECALIBRATOR_SNP.out.recal)
+        .join(VARIANTRECALIBRATOR_SNP.out.idx)
+        .join(VARIANTRECALIBRATOR_SNP.out.tranches)
+        .map{ meta, vcf, tbi, recal, index, tranche ->
+            new_meta = [
+                id:             "recalibrated_joint_variant_calling",
+                num_intervals:  meta.num_intervals,
+                patient:        "all_samples",
+                variantcaller:  "haplotypecaller",
+            ]
+            [new_meta, vcf, tbi, recal, index, tranche]
+        }
 
     //Join results of variant recalibration into a single channel tuple
     //Rework meta for variantscalled.csv and annotation tools
-    vqsr_input_indel = vqsr_input.join( VARIANTRECALIBRATOR_INDEL.out.recal).join(
-                                        VARIANTRECALIBRATOR_INDEL.out.idx).join(
-                                        VARIANTRECALIBRATOR_INDEL.out.tranches).map{ meta, vcf, tbi, recal, index, tranche ->
-
-                                                new_meta = [
-                                                            id:             "recalibrated_joint_variant_calling",
-                                                            num_intervals:  meta.num_intervals,
-                                                            patient:        "all_samples",
-                                                            variantcaller:  "haplotypecaller"
-                                                ]
-
-                                            [new_meta, vcf, tbi, recal, index, tranche]
-                                        }
-
-    GATK4_APPLYVQSR_SNP(vqsr_input_snp,
-                        fasta,
-                        fai,
-                        dict )
-
-    GATK4_APPLYVQSR_INDEL(vqsr_input_indel,
-                        fasta,
-                        fai,
-                        dict )
+    vqsr_input_indel = vqsr_input.join(VARIANTRECALIBRATOR_INDEL.out.recal)
+        .join(VARIANTRECALIBRATOR_INDEL.out.idx)
+        .join(VARIANTRECALIBRATOR_INDEL.out.tranches)
+        .map{ meta, vcf, tbi, recal, index, tranche ->
+            new_meta = [
+                id:             "recalibrated_joint_variant_calling",
+                num_intervals:  meta.num_intervals,
+                patient:        "all_samples",
+                variantcaller:  "haplotypecaller"
+            ]
+            [new_meta, vcf, tbi, recal, index, tranche]
+        }
+
+    GATK4_APPLYVQSR_SNP(
+        vqsr_input_snp,
+        fasta,
+        fai,
+        dict)
+
+    GATK4_APPLYVQSR_INDEL(
+        vqsr_input_indel,
+        fasta,
+        fai,
+        dict)
 
     vqsr_snp_vcf = GATK4_APPLYVQSR_SNP.out.vcf
     vqsr_indel_vcf = GATK4_APPLYVQSR_INDEL.out.vcf
@@ -183,7 +180,7 @@ workflow BAM_JOINT_CALLING_GERMLINE_GATK {
     //
     MERGE_VQSR(
         vqsr_snp_vcf.mix(vqsr_indel_vcf).groupTuple(),
-        dict
+        dict.map{ it -> [[id:it[0].baseName], it]}
     )
 
     ch_versions = ch_versions.mix(GATK4_GENOMICSDBIMPORT.out.versions)
@@ -191,8 +188,6 @@ workflow BAM_JOINT_CALLING_GERMLINE_GATK {
     ch_versions = ch_versions.mix(VARIANTRECALIBRATOR_SNP.out.versions)
     ch_versions = ch_versions.mix(GATK4_APPLYVQSR_SNP.out.versions)
 
-
-
     emit:
     versions       = ch_versions                                                                                            // channel: [ versions.yml ]
     genotype_vcf   = Channel.empty().mix( vcfs_sorted_input_no_intervals, MERGE_GENOTYPEGVCFS.out.vcf, MERGE_VQSR.out.vcf)  // channel: [ val(meta), [ vcf ] ]
diff --git a/subworkflows/local/bam_variant_calling_deepvariant/main.nf b/subworkflows/local/bam_variant_calling_deepvariant/main.nf
index 537d1d0d3f..f21ac5616f 100644
--- a/subworkflows/local/bam_variant_calling_deepvariant/main.nf
+++ b/subworkflows/local/bam_variant_calling_deepvariant/main.nf
@@ -49,7 +49,7 @@ workflow BAM_VARIANT_CALLING_DEEPVARIANT {
 
                 [groupKey(new_meta, meta.num_intervals), vcf]
             }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     MERGE_DEEPVARIANT_GVCF(
         deepvariant_gvcf_out.intervals
@@ -66,7 +66,7 @@ workflow BAM_VARIANT_CALLING_DEEPVARIANT {
 
                 [groupKey(new_meta, meta.num_intervals), vcf]
             }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     // Mix output channels for "no intervals" and "with intervals" results
     deepvariant_gvcf = Channel.empty().mix(
diff --git a/subworkflows/local/bam_variant_calling_freebayes/main.nf b/subworkflows/local/bam_variant_calling_freebayes/main.nf
index 148b20795e..750d3316db 100644
--- a/subworkflows/local/bam_variant_calling_freebayes/main.nf
+++ b/subworkflows/local/bam_variant_calling_freebayes/main.nf
@@ -52,8 +52,7 @@ workflow BAM_VARIANT_CALLING_FREEBAYES {
                                             ]
                 [groupKey(new_meta, meta.num_intervals), vcf]
             }.groupTuple(),
-        dict
-    )
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     // Mix output channels for "no intervals" and "with intervals" results
     freebayes_vcf = Channel.empty().mix(
diff --git a/subworkflows/local/bam_variant_calling_germline_manta/main.nf b/subworkflows/local/bam_variant_calling_germline_manta/main.nf
index 5fcbb0765d..5b322d8f6a 100644
--- a/subworkflows/local/bam_variant_calling_germline_manta/main.nf
+++ b/subworkflows/local/bam_variant_calling_germline_manta/main.nf
@@ -49,7 +49,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_MANTA {
                         meta.num_intervals),
                 vcf]
             }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     MERGE_MANTA_SV(
         manta_sv_vcf.intervals
@@ -67,7 +67,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_MANTA {
                 vcf]
 
             }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     MERGE_MANTA_DIPLOID(
         manta_diploid_sv_vcf.intervals
@@ -85,7 +85,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_MANTA {
                 vcf]
 
             }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     // Mix output channels for "no intervals" and "with intervals" results
     // Only diploid SV should get annotated
diff --git a/subworkflows/local/bam_variant_calling_haplotypecaller/main.nf b/subworkflows/local/bam_variant_calling_haplotypecaller/main.nf
index ebf13d2d47..3efaa2948c 100644
--- a/subworkflows/local/bam_variant_calling_haplotypecaller/main.nf
+++ b/subworkflows/local/bam_variant_calling_haplotypecaller/main.nf
@@ -97,7 +97,7 @@ workflow BAM_VARIANT_CALLING_HAPLOTYPECALLER {
 
                     [groupKey(new_meta, new_meta.num_intervals), vcf]
                 }.groupTuple(),
-            dict)
+            dict.map{ it -> [[id:it[0].baseName], it]})
 
         haplotypecaller_vcf = Channel.empty().mix(
             MERGE_HAPLOTYPECALLER.out.vcf,
diff --git a/subworkflows/local/bam_variant_calling_mpileup/main.nf b/subworkflows/local/bam_variant_calling_mpileup/main.nf
index 211b206388..c72223b3e4 100644
--- a/subworkflows/local/bam_variant_calling_mpileup/main.nf
+++ b/subworkflows/local/bam_variant_calling_mpileup/main.nf
@@ -62,7 +62,7 @@ workflow BAM_VARIANT_CALLING_MPILEUP {
 
             [groupKey(new_meta, new_meta.num_intervals), vcf]
         }.groupTuple(),
-    dict)
+    dict.map{ it -> [[id:it[0].baseName], it]})
 
     ch_versions = ch_versions.mix(SAMTOOLS_MPILEUP.out.versions)
     ch_versions = ch_versions.mix(BCFTOOLS_MPILEUP.out.versions)
diff --git a/subworkflows/local/bam_variant_calling_single_strelka/main.nf b/subworkflows/local/bam_variant_calling_single_strelka/main.nf
index a7e0f641c3..77a7f0b7d3 100644
--- a/subworkflows/local/bam_variant_calling_single_strelka/main.nf
+++ b/subworkflows/local/bam_variant_calling_single_strelka/main.nf
@@ -40,8 +40,7 @@ workflow BAM_VARIANT_CALLING_SINGLE_STRELKA {
 
                 [groupKey(new_meta, meta.num_intervals), vcf]
             }.groupTuple(),
-        dict
-    )
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     MERGE_STRELKA_GENOME(
         strelka_genome_vcf.intervals
@@ -59,8 +58,7 @@ workflow BAM_VARIANT_CALLING_SINGLE_STRELKA {
                 vcf]
 
             }.groupTuple(),
-        dict
-    )
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     // Mix output channels for "no intervals" and "with intervals" results
     // Only strelka variant vcf should get annotated
diff --git a/subworkflows/local/bam_variant_calling_somatic_manta/main.nf b/subworkflows/local/bam_variant_calling_somatic_manta/main.nf
index bee724e395..8bca21cfb7 100644
--- a/subworkflows/local/bam_variant_calling_somatic_manta/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_manta/main.nf
@@ -59,7 +59,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MANTA {
                 vcf]
 
             }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     MERGE_MANTA_SMALL_INDELS(
         manta_candidate_sv_vcf.intervals.map{ meta, vcf ->
@@ -76,7 +76,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MANTA {
                 vcf]
 
             }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     MERGE_MANTA_DIPLOID(
         manta_diploid_sv_vcf.intervals.map{ meta, vcf ->
@@ -101,7 +101,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MANTA {
                 vcf]
 
             }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     MERGE_MANTA_SOMATIC(
         manta_somatic_sv_vcf.intervals.map{ meta, vcf ->
@@ -118,7 +118,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MANTA {
                 vcf]
 
             }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     // Mix output channels for "no intervals" and "with intervals" results
     manta_vcf = Channel.empty().mix(
diff --git a/subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf b/subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf
index a2e09ebfab..3418f7bb84 100644
--- a/subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf
@@ -76,8 +76,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MUTECT2 {
 
             [groupKey(new_meta, meta.num_intervals), vcf]
         }.groupTuple(),
-        dict
-    )
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     mutect2_vcf = Channel.empty().mix(
         MERGE_MUTECT2.out.vcf,
diff --git a/subworkflows/local/bam_variant_calling_somatic_strelka/main.nf b/subworkflows/local/bam_variant_calling_somatic_strelka/main.nf
index 003c9a73c6..74346897a8 100644
--- a/subworkflows/local/bam_variant_calling_somatic_strelka/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_strelka/main.nf
@@ -41,7 +41,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_STRELKA {
                 vcf]
 
             }.groupTuple(),
-            dict)
+            dict.map{ it -> [[id:it[0].baseName], it]})
 
     MERGE_STRELKA_INDELS(strelka_vcf_indels.intervals.map{ meta, vcf ->
 
@@ -56,7 +56,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_STRELKA {
                             meta.num_intervals),
                 vcf]
             }.groupTuple(),
-            dict)
+            dict.map{ it -> [[id:it[0].baseName], it]})
 
     // Mix output channels for "no intervals" and "with intervals" results
     strelka_vcf = Channel.empty().mix(
diff --git a/subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf
index f0351334f7..793641669e 100644
--- a/subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf
+++ b/subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf
@@ -49,7 +49,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA {
                 vcf]
 
             }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     MERGE_MANTA_SV(
         manta_candidate_sv_vcf.intervals.map{ meta, vcf ->
@@ -66,7 +66,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA {
                 vcf]
 
             }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     MERGE_MANTA_TUMOR(
         manta_tumor_sv_vcf.intervals.map{ meta, vcf ->
@@ -83,7 +83,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_MANTA {
                 vcf]
 
             }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     // Mix output channels for "no intervals" and "with intervals" results
     // Only tumor sv should get annotated
diff --git a/subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf b/subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf
index eae2a2b24e..c681c150b2 100644
--- a/subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf
+++ b/subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf
@@ -75,7 +75,7 @@ workflow BAM_VARIANT_CALLING_TUMOR_ONLY_MUTECT2 {
 
             [groupKey(new_meta, meta.num_intervals), vcf]
         }.groupTuple(),
-        dict)
+        dict.map{ it -> [[id:it[0].baseName], it]})
 
     mutect2_vcf = Channel.empty().mix(
         MERGE_MUTECT2.out.vcf,
diff --git a/tests/config/pytest_tags.yml b/tests/config/pytest_tags.yml
index ed429079d8..717b3f09ed 100644
--- a/tests/config/pytest_tags.yml
+++ b/tests/config/pytest_tags.yml
@@ -1,6 +1,38 @@
 # default_extended
 
-default_extended:
+tumor_normal_pair:
+  - conf/modules/**
+  - modules/**
+  - subworkflows/**
+  - workflows/**
+  - nextflow.config
+  - main.nf
+
+save_mapped_only:
+  - conf/modules/**
+  - modules/**
+  - subworkflows/**
+  - workflows/**
+  - nextflow.config
+  - main.nf
+
+save_output_as_bam_only:
+  - conf/modules/**
+  - modules/**
+  - subworkflows/**
+  - workflows/**
+  - nextflow.config
+  - main.nf
+
+skip_all_qc:
+  - conf/modules/**
+  - modules/**
+  - subworkflows/**
+  - workflows/**
+  - nextflow.config
+  - main.nf
+
+skip_markduplicates:
   - conf/modules/**
   - modules/**
   - subworkflows/**
diff --git a/tests/test_default_extended.yml b/tests/test_default_extended.yml
deleted file mode 100644
index 958627a963..0000000000
--- a/tests/test_default_extended.yml
+++ /dev/null
@@ -1,446 +0,0 @@
-- name: Run save_mapped
-  command: nextflow run main.nf -profile test --save_mapped
-  tags:
-    - default_extended
-    - preprocessing
-    - save_mapped
-    - variant_calling
-  files:
-    - path: results/csv/mapped.csv
-      md5sum: 3bee45ccf65e301ce09ee4eed8f26933
-    - path: results/csv/markduplicates.csv
-      md5sum: 0d6120bb99e92f6810343270711ca53e
-    - path: results/csv/markduplicates_no_table.csv
-      md5sum: 2a2d3d4842befd4def39156463859ee3
-    - path: results/csv/recalibrated.csv
-      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
-    - path: results/multiqc
-    - path: results/preprocessing/mapped/test/test.sorted.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/mapped/test/test.sorted.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/markduplicates/test/test.md.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recal_table/test/test.recal.table
-      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
-    - path: results/preprocessing/recalibrated/test/test.recal.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/markduplicates/test/test.md.cram.metrics
-      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
-    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
-      md5sum: b1c2a861f64e20a94108a6de3b76c582
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-      md5sum: b1c2a861f64e20a94108a6de3b76c582
-    - path: results/reports/samtools/test/test.md.cram.stats
-    # conda changes md5sums for test.
-    - path: results/reports/samtools/test/test.recal.cram.stats
-    # conda changes md5sums for test.
-    - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt
-    # conda changes md5sums for test.
-    - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary
-      md5sum: dd87f507da7de20d5318841af312493b
-    - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count
-      md5sum: fa27f678965b7cba6a92efcd039f802a
-    - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual
-      md5sum: bc68ae4e688e9fb772b457069e604883
-    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
-    # binary changes md5sums on reruns.
-    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
-    # binary changes md5sums on reruns.
-    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
-    # binary changes md5sums on reruns.
-    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
-    - path: results/strelka
-      should_exist: false
-- name: Run save_output_as_bam
-  command: nextflow run main.nf -profile test --save_output_as_bam
-  tags:
-    - default_extended
-    - preprocessing
-    - save_output_as_bam
-    - variant_calling
-  files:
-    - path: results/csv/markduplicates.csv
-      md5sum: 6004ab16b63012e336f6251396a983c5
-    - path: results/csv/markduplicates_no_table.csv
-      md5sum: 8a145eca178cfd02403d60122b9d3960
-    - path: results/csv/recalibrated.csv
-      md5sum: 2dfbcaaeaaf4937c51c5c310f1c77614
-    - path: results/multiqc
-    - path: results/preprocessing/markduplicates/test/test.md.bam.bai
-    # conda changes md5sums for test.
-    - path: results/preprocessing/markduplicates/test/test.md.bam
-    # conda changes md5sums for test.
-    - path: results/preprocessing/recal_table/test/test.recal.table
-      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
-    - path: results/preprocessing/recalibrated/test/test.recal.bam
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recalibrated/test/test.recal.bam.bai
-    # binary changes md5sums on reruns.
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/markduplicates/test/test.md.cram.metrics
-      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
-    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
-      md5sum: b1c2a861f64e20a94108a6de3b76c582
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-      md5sum: b1c2a861f64e20a94108a6de3b76c582
-    - path: results/reports/samtools/test/test.md.cram.stats
-    # conda changes md5sums for test.
-    - path: results/reports/samtools/test/test.recal.cram.stats
-    # conda changes md5sums for test.
-    - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt
-    # conda changes md5sums for test.
-    - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary
-      md5sum: dd87f507da7de20d5318841af312493b
-    - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count
-      md5sum: fa27f678965b7cba6a92efcd039f802a
-    - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual
-      md5sum: bc68ae4e688e9fb772b457069e604883
-    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
-    # binary changes md5sums on reruns.
-    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
-    # binary changes md5sums on reruns.
-    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
-    # binary changes md5sums on reruns.
-    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
-    - path: results/strelka
-      should_exist: false
-- name: Run default pipeline with skipping Markduplicates
-  command: nextflow run main.nf -profile test,skip_markduplicates
-  tags:
-    - default_extended
-    - preprocessing
-    - skip_markduplicates
-  files:
-    - path: results/csv/mapped.csv
-      md5sum: 3bee45ccf65e301ce09ee4eed8f26933
-    - path: results/csv/recalibrated.csv
-      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
-    - path: results/multiqc
-    - path: results/preprocessing/mapped/test/test.sorted.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/mapped/test/test.sorted.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recal_table/test/test.recal.table
-      md5sum: 8de213f4c00fac61a1102633760493df
-    - path: results/preprocessing/recalibrated/test/test.recal.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: 48aa760b024d7c0ddd5a66f89a1cb544
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: 71e938314bba70f978271b2b56cb7ad3
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: 0786d56af0672eaef44b29f4ed5c12cb
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: b8719430e56a58f734884bb422a7b8fa
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-      md5sum: e3235323f455414ee3acc7144e659caf
-    - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt
-      md5sum: 48aa760b024d7c0ddd5a66f89a1cb544
-    - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt
-      md5sum: 71e938314bba70f978271b2b56cb7ad3
-    - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt
-      md5sum: 0786d56af0672eaef44b29f4ed5c12cb
-    - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
-      md5sum: b8719430e56a58f734884bb422a7b8fa
-    - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
-      md5sum: e3235323f455414ee3acc7144e659caf
-    - path: results/reports/samtools/test/test.recal.cram.stats
-    # conda changes md5sums for test.
-    - path: results/reports/samtools/test/test.sorted.cram.stats
-    # conda changes md5sums for test.
-    - path: results/csv/markduplicates.csv
-      should_exist: false
-    - path: results/csv/markduplicates_no_table.csv
-      should_exist: false
-    - path: results/preprocessing/mapped/test/test.bam
-      should_exist: false
-    - path: results/preprocessing/mapped/test/test.sorted.bam
-      should_exist: false
-- name: Run default pipeline with skipping Markduplicates with save_mapped
-  command: nextflow run main.nf -profile test,skip_markduplicates --save_mapped
-  tags:
-    - default_extended
-    - preprocessing
-    - save_mapped
-  files:
-    - path: results/csv/mapped.csv
-      md5sum: 3bee45ccf65e301ce09ee4eed8f26933
-    - path: results/csv/recalibrated.csv
-      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
-    - path: results/multiqc
-    - path: results/preprocessing/mapped/test/test.sorted.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/mapped/test/test.sorted.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recal_table/test/test.recal.table
-      md5sum: 8de213f4c00fac61a1102633760493df
-    - path: results/preprocessing/recalibrated/test/test.recal.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: 48aa760b024d7c0ddd5a66f89a1cb544
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: 71e938314bba70f978271b2b56cb7ad3
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: 0786d56af0672eaef44b29f4ed5c12cb
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: b8719430e56a58f734884bb422a7b8fa
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-      md5sum: e3235323f455414ee3acc7144e659caf
-    - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt
-      md5sum: 48aa760b024d7c0ddd5a66f89a1cb544
-    - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt
-      md5sum: 71e938314bba70f978271b2b56cb7ad3
-    - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt
-      md5sum: 0786d56af0672eaef44b29f4ed5c12cb
-    - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
-      md5sum: b8719430e56a58f734884bb422a7b8fa
-    - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
-      md5sum: e3235323f455414ee3acc7144e659caf
-    - path: results/reports/samtools/test/test.recal.cram.stats
-    # conda changes md5sums for test.
-    - path: results/reports/samtools/test/test.sorted.cram.stats
-    # conda changes md5sums for test.
-    - path: results/csv/markduplicates.csv
-      should_exist: false
-    - path: results/csv/markduplicates_no_table.csv
-      should_exist: false
-    - path: results/preprocessing/mapped/test/test.bam
-      should_exist: false
-- name: Run default pipeline with skipping Markduplicates with save_mapped & save_output_as_bam
-  command: nextflow run main.nf -profile test,skip_markduplicates --save_mapped --save_output_as_bam
-  tags:
-    - default_extended
-    - preprocessing
-    - save_output_as_bam
-  files:
-    - path: results/csv/mapped.csv
-      md5sum: 7f21bf40d3fbc248ee2ea3fdf0f7cdb2
-    - path: results/csv/recalibrated.csv
-      md5sum: 2dfbcaaeaaf4937c51c5c310f1c77614
-    - path: results/multiqc
-    - path: results/preprocessing/mapped/test/test.sorted.bam
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/mapped/test/test.sorted.bam.bai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recal_table/test/test.recal.table
-      md5sum: 8de213f4c00fac61a1102633760493df
-    - path: results/preprocessing/recalibrated/test/test.recal.bam
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recalibrated/test/test.recal.bam.bai
-    # binary changes md5sums on reruns.
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: 48aa760b024d7c0ddd5a66f89a1cb544
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: 71e938314bba70f978271b2b56cb7ad3
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: 0786d56af0672eaef44b29f4ed5c12cb
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: b8719430e56a58f734884bb422a7b8fa
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-      md5sum: e3235323f455414ee3acc7144e659caf
-    - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt
-      md5sum: 48aa760b024d7c0ddd5a66f89a1cb544
-    - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt
-      md5sum: 71e938314bba70f978271b2b56cb7ad3
-    - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt
-      md5sum: 0786d56af0672eaef44b29f4ed5c12cb
-    - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
-      md5sum: b8719430e56a58f734884bb422a7b8fa
-    - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
-      md5sum: e3235323f455414ee3acc7144e659caf
-    - path: results/reports/samtools/test/test.recal.cram.stats
-    # conda changes md5sums for test.
-    - path: results/reports/samtools/test/test.sorted.cram.stats
-    # conda changes md5sums for test.
-    - path: results/csv/markduplicates.csv
-      should_exist: false
-    - path: results/csv/markduplicates_no_table.csv
-      should_exist: false
-    - path: results/preprocessing/mapped/test/test.bam
-      should_exist: false
-- name: Run default pipeline with skipping all QC steps
-  command: nextflow run main.nf -profile test --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools
-  tags:
-    - default_extended
-    - preprocessing
-    - skip_qc
-    - variant_calling
-  files:
-    - path: results/csv/markduplicates.csv
-      md5sum: 0d6120bb99e92f6810343270711ca53e
-    - path: results/csv/markduplicates_no_table.csv
-      md5sum: 2a2d3d4842befd4def39156463859ee3
-    - path: results/csv/recalibrated.csv
-      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
-    - path: results/preprocessing/markduplicates/test/test.md.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recal_table/test/test.recal.table
-      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
-    - path: results/preprocessing/recalibrated/test/test.recal.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/multiqc
-      should_exist: false
-    - path: results/reports/fastqc
-      should_exist: false
-    - path: results/reports/markduplicates
-      should_exist: false
-    - path: results/reports/mosdepth
-      should_exist: false
-    - path: results/reports/samtools
-      should_exist: false
-    - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt
-    # conda changes md5sums for test.
-    - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary
-      md5sum: dd87f507da7de20d5318841af312493b
-    - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count
-      md5sum: fa27f678965b7cba6a92efcd039f802a
-    - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual
-      md5sum: bc68ae4e688e9fb772b457069e604883
-    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
-    # binary changes md5sums on reruns.
-    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
-    # binary changes md5sums on reruns.
-    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
-    # binary changes md5sums on reruns.
-    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
-    - path: results/strelka
-      should_exist: false
-- name: Run default pipeline for tumor normal pair
-  command: nextflow run main.nf -profile test,pair
-  tags:
-    - default_extended
-    - preprocessing
-    - tumor_normal_pair
-  files:
-    - path: results/csv/markduplicates.csv
-      md5sum: e8e587ac25253ff7ab8f1cc66d410c98
-    - path: results/csv/markduplicates_no_table.csv
-      md5sum: 617574c9b607e5daaf4ad56d48982247
-    - path: results/csv/recalibrated.csv
-      md5sum: 008dff17e2a0d96ef9c1cae12fcab6ab
-    - path: results/multiqc
-    - path: results/preprocessing/markduplicates/test/test.md.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recal_table/test/test.recal.table
-      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
-    - path: results/preprocessing/recalibrated/test/test.recal.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/markduplicates/test2/test2.md.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/markduplicates/test2/test2.md.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recal_table/test2/test2.recal.table
-      md5sum: 0626cd4337eab79b38b5bc5c95e0c003
-    - path: results/preprocessing/recalibrated/test2/test2.recal.cram
-    # binary changes md5sums on reruns.
-    - path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai
-    # binary changes md5sums on reruns.
-    - path: results/reports/fastqc/test-test_L1
-    - path: results/reports/fastqc/test2-test_L1
-    - path: results/reports/markduplicates/test/test.md.cram.metrics
-      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
-    - path: results/reports/markduplicates/test2/test2.md.cram.metrics
-      contains: ["test2	10103	880	35	523579	4837	2	0	0.408076	193306", "1.0	1	876	876", "100.0	80.515303	0	0"]
-    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
-      md5sum: b1c2a861f64e20a94108a6de3b76c582
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
-      md5sum: 76fa71922a3f748e507c2364c531dfcb
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
-      md5sum: abc5df85e302b79985627888870882da
-    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
-      md5sum: d536456436eb275159b8c6af83213d80
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
-      md5sum: 38fe39894abe62e38f8ac214cba64f2b
-    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
-      md5sum: b1c2a861f64e20a94108a6de3b76c582
-    - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
-      md5sum: 2020cf6dfc7ddca020c921dd9f0549b7
-    - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt
-      md5sum: 38ff8b38c33b9231f047fea8ea830aae
-    - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
-      md5sum: 8b991358768cade225470a07cd34f573
-    - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz
-      md5sum: 5d67bc6ea9f077abb4fdac3b087c6387
-    - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi
-      md5sum: d5f1c9389ecf52ba839e834780a94549
-    - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
-      md5sum: 2020cf6dfc7ddca020c921dd9f0549b7
-    - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt
-      md5sum: 38ff8b38c33b9231f047fea8ea830aae
-    - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
-      md5sum: 8b991358768cade225470a07cd34f573
-    - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz
-      md5sum: 5d67bc6ea9f077abb4fdac3b087c6387
-    - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi
-      md5sum: d5f1c9389ecf52ba839e834780a94549
-    - path: results/reports/samtools/test/test.md.cram.stats
-    # conda changes md5sums for test.
-    - path: results/reports/samtools/test/test.recal.cram.stats
-    # conda changes md5sums for test.
-    - path: results/reports/samtools/test2/test2.md.cram.stats
-    # conda changes md5sums for test.
-    - path: results/reports/samtools/test2/test2.recal.cram.stats
-    # conda changes md5sums for test.
-    - path: results/preprocessing/mapped/
-      should_exist: false
diff --git a/tests/test_save_mapped.yml b/tests/test_save_mapped.yml
new file mode 100644
index 0000000000..a49422665c
--- /dev/null
+++ b/tests/test_save_mapped.yml
@@ -0,0 +1,76 @@
+- name: Run save_mapped
+  command: nextflow run main.nf -profile test --save_mapped
+  tags:
+    - default_extended
+    - preprocessing
+    - save_mapped
+    - save_mapped_only
+    - variant_calling
+  files:
+    - path: results/csv/mapped.csv
+      md5sum: 3bee45ccf65e301ce09ee4eed8f26933
+    - path: results/csv/markduplicates.csv
+      md5sum: 0d6120bb99e92f6810343270711ca53e
+    - path: results/csv/markduplicates_no_table.csv
+      md5sum: 2a2d3d4842befd4def39156463859ee3
+    - path: results/csv/recalibrated.csv
+      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
+    - path: results/multiqc
+    - path: results/preprocessing/mapped/test/test.sorted.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/mapped/test/test.sorted.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recal_table/test/test.recal.table
+      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/reports/fastqc/test-test_L1
+    - path: results/reports/markduplicates/test/test.md.cram.metrics
+      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
+      md5sum: b1c2a861f64e20a94108a6de3b76c582
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: b1c2a861f64e20a94108a6de3b76c582
+    - path: results/reports/samtools/test/test.md.cram.stats
+    # conda changes md5sums for test.
+    - path: results/reports/samtools/test/test.recal.cram.stats
+    # conda changes md5sums for test.
+    - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt
+    # conda changes md5sums for test.
+    - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary
+      md5sum: dd87f507da7de20d5318841af312493b
+    - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count
+      md5sum: fa27f678965b7cba6a92efcd039f802a
+    - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual
+      md5sum: bc68ae4e688e9fb772b457069e604883
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    # binary changes md5sums on reruns.
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    # binary changes md5sums on reruns.
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    # binary changes md5sums on reruns.
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
+    - path: results/strelka
+      should_exist: false
diff --git a/tests/test_save_output_as_bam_only.yml b/tests/test_save_output_as_bam_only.yml
new file mode 100644
index 0000000000..374cdeb69e
--- /dev/null
+++ b/tests/test_save_output_as_bam_only.yml
@@ -0,0 +1,70 @@
+- name: Run save_output_as_bam
+  command: nextflow run main.nf -profile test --save_output_as_bam
+  tags:
+    - default_extended
+    - preprocessing
+    - save_output_as_bam
+    - save_output_as_bam_only
+    - variant_calling
+  files:
+    - path: results/csv/markduplicates.csv
+      md5sum: 6004ab16b63012e336f6251396a983c5
+    - path: results/csv/markduplicates_no_table.csv
+      md5sum: 8a145eca178cfd02403d60122b9d3960
+    - path: results/csv/recalibrated.csv
+      md5sum: 2dfbcaaeaaf4937c51c5c310f1c77614
+    - path: results/multiqc
+    - path: results/preprocessing/markduplicates/test/test.md.bam.bai
+    # conda changes md5sums for test.
+    - path: results/preprocessing/markduplicates/test/test.md.bam
+    # conda changes md5sums for test.
+    - path: results/preprocessing/recal_table/test/test.recal.table
+      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
+    - path: results/preprocessing/recalibrated/test/test.recal.bam
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recalibrated/test/test.recal.bam.bai
+    # binary changes md5sums on reruns.
+    - path: results/reports/fastqc/test-test_L1
+    - path: results/reports/markduplicates/test/test.md.cram.metrics
+      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
+      md5sum: b1c2a861f64e20a94108a6de3b76c582
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: b1c2a861f64e20a94108a6de3b76c582
+    - path: results/reports/samtools/test/test.md.cram.stats
+    # conda changes md5sums for test.
+    - path: results/reports/samtools/test/test.recal.cram.stats
+    # conda changes md5sums for test.
+    - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt
+    # conda changes md5sums for test.
+    - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary
+      md5sum: dd87f507da7de20d5318841af312493b
+    - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count
+      md5sum: fa27f678965b7cba6a92efcd039f802a
+    - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual
+      md5sum: bc68ae4e688e9fb772b457069e604883
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    # binary changes md5sums on reruns.
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    # binary changes md5sums on reruns.
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    # binary changes md5sums on reruns.
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
+    - path: results/strelka
+      should_exist: false
diff --git a/tests/test_skip_all_qc.yml b/tests/test_skip_all_qc.yml
new file mode 100644
index 0000000000..c65758c000
--- /dev/null
+++ b/tests/test_skip_all_qc.yml
@@ -0,0 +1,52 @@
+- name: Run default pipeline with skipping all QC steps
+  command: nextflow run main.nf -profile test --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools
+  tags:
+    - default_extended
+    - preprocessing
+    - skip_all_qc
+    - skip_qc
+    - variant_calling
+  files:
+    - path: results/csv/markduplicates.csv
+      md5sum: 0d6120bb99e92f6810343270711ca53e
+    - path: results/csv/markduplicates_no_table.csv
+      md5sum: 2a2d3d4842befd4def39156463859ee3
+    - path: results/csv/recalibrated.csv
+      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recal_table/test/test.recal.table
+      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/multiqc
+      should_exist: false
+    - path: results/reports/fastqc
+      should_exist: false
+    - path: results/reports/markduplicates
+      should_exist: false
+    - path: results/reports/mosdepth
+      should_exist: false
+    - path: results/reports/samtools
+      should_exist: false
+    - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt
+    # conda changes md5sums for test.
+    - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary
+      md5sum: dd87f507da7de20d5318841af312493b
+    - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count
+      md5sum: fa27f678965b7cba6a92efcd039f802a
+    - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual
+      md5sum: bc68ae4e688e9fb772b457069e604883
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz
+    # binary changes md5sums on reruns.
+    - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi
+    # binary changes md5sums on reruns.
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz
+    # binary changes md5sums on reruns.
+    - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi
+    - path: results/strelka
+      should_exist: false
diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml
new file mode 100644
index 0000000000..f98e1077d2
--- /dev/null
+++ b/tests/test_skip_markduplicates.yml
@@ -0,0 +1,163 @@
+- name: Run default pipeline with skipping Markduplicates
+  command: nextflow run main.nf -profile test,skip_markduplicates
+  tags:
+    - default_extended
+    - preprocessing
+    - skip_markduplicates
+  files:
+    - path: results/csv/mapped.csv
+      md5sum: 3bee45ccf65e301ce09ee4eed8f26933
+    - path: results/csv/recalibrated.csv
+      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
+    - path: results/multiqc
+    - path: results/preprocessing/mapped/test/test.sorted.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/mapped/test/test.sorted.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recal_table/test/test.recal.table
+      md5sum: 8de213f4c00fac61a1102633760493df
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/reports/fastqc/test-test_L1
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: 48aa760b024d7c0ddd5a66f89a1cb544
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 71e938314bba70f978271b2b56cb7ad3
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 0786d56af0672eaef44b29f4ed5c12cb
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: b8719430e56a58f734884bb422a7b8fa
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: e3235323f455414ee3acc7144e659caf
+    - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt
+      md5sum: 48aa760b024d7c0ddd5a66f89a1cb544
+    - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt
+      md5sum: 71e938314bba70f978271b2b56cb7ad3
+    - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt
+      md5sum: 0786d56af0672eaef44b29f4ed5c12cb
+    - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
+      md5sum: b8719430e56a58f734884bb422a7b8fa
+    - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
+      md5sum: e3235323f455414ee3acc7144e659caf
+    - path: results/reports/samtools/test/test.recal.cram.stats
+    # conda changes md5sums for test.
+    - path: results/reports/samtools/test/test.sorted.cram.stats
+    # conda changes md5sums for test.
+    - path: results/csv/markduplicates.csv
+      should_exist: false
+    - path: results/csv/markduplicates_no_table.csv
+      should_exist: false
+    - path: results/preprocessing/mapped/test/test.bam
+      should_exist: false
+    - path: results/preprocessing/mapped/test/test.sorted.bam
+      should_exist: false
+- name: Run default pipeline with skipping Markduplicates with save_mapped
+  command: nextflow run main.nf -profile test,skip_markduplicates --save_mapped
+  tags:
+    - default_extended
+    - preprocessing
+    - save_mapped
+    - skip_markduplicates
+  files:
+    - path: results/csv/mapped.csv
+      md5sum: 3bee45ccf65e301ce09ee4eed8f26933
+    - path: results/csv/recalibrated.csv
+      md5sum: 2d29d9e53894dcce96a1b5beb6ef3312
+    - path: results/multiqc
+    - path: results/preprocessing/mapped/test/test.sorted.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/mapped/test/test.sorted.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recal_table/test/test.recal.table
+      md5sum: 8de213f4c00fac61a1102633760493df
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/reports/fastqc/test-test_L1
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: 48aa760b024d7c0ddd5a66f89a1cb544
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 71e938314bba70f978271b2b56cb7ad3
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 0786d56af0672eaef44b29f4ed5c12cb
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: b8719430e56a58f734884bb422a7b8fa
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: e3235323f455414ee3acc7144e659caf
+    - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt
+      md5sum: 48aa760b024d7c0ddd5a66f89a1cb544
+    - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt
+      md5sum: 71e938314bba70f978271b2b56cb7ad3
+    - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt
+      md5sum: 0786d56af0672eaef44b29f4ed5c12cb
+    - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
+      md5sum: b8719430e56a58f734884bb422a7b8fa
+    - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
+      md5sum: e3235323f455414ee3acc7144e659caf
+    - path: results/reports/samtools/test/test.recal.cram.stats
+    # conda changes md5sums for test.
+    - path: results/reports/samtools/test/test.sorted.cram.stats
+    # conda changes md5sums for test.
+    - path: results/csv/markduplicates.csv
+      should_exist: false
+    - path: results/csv/markduplicates_no_table.csv
+      should_exist: false
+    - path: results/preprocessing/mapped/test/test.bam
+      should_exist: false
+- name: Run default pipeline with skipping Markduplicates with save_mapped & save_output_as_bam
+  command: nextflow run main.nf -profile test,skip_markduplicates --save_mapped --save_output_as_bam
+  tags:
+    - default_extended
+    - preprocessing
+    - save_output_as_bam
+    - skip_markduplicates
+  files:
+    - path: results/csv/mapped.csv
+      md5sum: 7f21bf40d3fbc248ee2ea3fdf0f7cdb2
+    - path: results/csv/recalibrated.csv
+      md5sum: 2dfbcaaeaaf4937c51c5c310f1c77614
+    - path: results/multiqc
+    - path: results/preprocessing/mapped/test/test.sorted.bam
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/mapped/test/test.sorted.bam.bai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recal_table/test/test.recal.table
+      md5sum: 8de213f4c00fac61a1102633760493df
+    - path: results/preprocessing/recalibrated/test/test.recal.bam
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recalibrated/test/test.recal.bam.bai
+    # binary changes md5sums on reruns.
+    - path: results/reports/fastqc/test-test_L1
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: 48aa760b024d7c0ddd5a66f89a1cb544
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 71e938314bba70f978271b2b56cb7ad3
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 0786d56af0672eaef44b29f4ed5c12cb
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: b8719430e56a58f734884bb422a7b8fa
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: e3235323f455414ee3acc7144e659caf
+    - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt
+      md5sum: 48aa760b024d7c0ddd5a66f89a1cb544
+    - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt
+      md5sum: 71e938314bba70f978271b2b56cb7ad3
+    - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt
+      md5sum: 0786d56af0672eaef44b29f4ed5c12cb
+    - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz
+      md5sum: b8719430e56a58f734884bb422a7b8fa
+    - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi
+      md5sum: e3235323f455414ee3acc7144e659caf
+    - path: results/reports/samtools/test/test.recal.cram.stats
+    # conda changes md5sums for test.
+    - path: results/reports/samtools/test/test.sorted.cram.stats
+    # conda changes md5sums for test.
+    - path: results/csv/markduplicates.csv
+      should_exist: false
+    - path: results/csv/markduplicates_no_table.csv
+      should_exist: false
+    - path: results/preprocessing/mapped/test/test.bam
+      should_exist: false
diff --git a/tests/test_tumor_normal_pair.yml b/tests/test_tumor_normal_pair.yml
new file mode 100644
index 0000000000..297a91a6d8
--- /dev/null
+++ b/tests/test_tumor_normal_pair.yml
@@ -0,0 +1,90 @@
+- name: Run default pipeline for tumor normal pair
+  command: nextflow run main.nf -profile test,pair
+  tags:
+    - default_extended
+    - preprocessing
+    - tumor_normal_pair
+  files:
+    - path: results/csv/markduplicates.csv
+      md5sum: e8e587ac25253ff7ab8f1cc66d410c98
+    - path: results/csv/markduplicates_no_table.csv
+      md5sum: 617574c9b607e5daaf4ad56d48982247
+    - path: results/csv/recalibrated.csv
+      md5sum: 008dff17e2a0d96ef9c1cae12fcab6ab
+    - path: results/multiqc
+    - path: results/preprocessing/markduplicates/test/test.md.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/markduplicates/test/test.md.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recal_table/test/test.recal.table
+      md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe
+    - path: results/preprocessing/recalibrated/test/test.recal.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/markduplicates/test2/test2.md.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/markduplicates/test2/test2.md.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recal_table/test2/test2.recal.table
+      md5sum: 0626cd4337eab79b38b5bc5c95e0c003
+    - path: results/preprocessing/recalibrated/test2/test2.recal.cram
+    # binary changes md5sums on reruns.
+    - path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai
+    # binary changes md5sums on reruns.
+    - path: results/reports/fastqc/test-test_L1
+    - path: results/reports/fastqc/test2-test_L1
+    - path: results/reports/markduplicates/test/test.md.cram.metrics
+      contains: ["test	8547	767	84	523391	3882	0	0	0.385081", "1.0	767	767"]
+    - path: results/reports/markduplicates/test2/test2.md.cram.metrics
+      contains: ["test2	10103	880	35	523579	4837	2	0	0.408076	193306", "1.0	1	876	876", "100.0	80.515303	0	0"]
+    - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi
+      md5sum: b1c2a861f64e20a94108a6de3b76c582
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: 76fa71922a3f748e507c2364c531dfcb
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: abc5df85e302b79985627888870882da
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: d536456436eb275159b8c6af83213d80
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 38fe39894abe62e38f8ac214cba64f2b
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: b1c2a861f64e20a94108a6de3b76c582
+    - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt
+      md5sum: 2020cf6dfc7ddca020c921dd9f0549b7
+    - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt
+      md5sum: 38ff8b38c33b9231f047fea8ea830aae
+    - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt
+      md5sum: 8b991358768cade225470a07cd34f573
+    - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz
+      md5sum: 5d67bc6ea9f077abb4fdac3b087c6387
+    - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi
+      md5sum: d5f1c9389ecf52ba839e834780a94549
+    - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt
+      md5sum: 2020cf6dfc7ddca020c921dd9f0549b7
+    - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt
+      md5sum: 38ff8b38c33b9231f047fea8ea830aae
+    - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt
+      md5sum: 8b991358768cade225470a07cd34f573
+    - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz
+      md5sum: 5d67bc6ea9f077abb4fdac3b087c6387
+    - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi
+      md5sum: d5f1c9389ecf52ba839e834780a94549
+    - path: results/reports/samtools/test/test.md.cram.stats
+    # conda changes md5sums for test.
+    - path: results/reports/samtools/test/test.recal.cram.stats
+    # conda changes md5sums for test.
+    - path: results/reports/samtools/test2/test2.md.cram.stats
+    # conda changes md5sums for test.
+    - path: results/reports/samtools/test2/test2.recal.cram.stats
+    # conda changes md5sums for test.
+    - path: results/preprocessing/mapped/
+      should_exist: false