diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4826d3015e..baf7361613 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -48,6 +48,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#520](https://github.com/nf-core/sarek/pull/520) - Improve annotation subworkflows
 - [#537](https://github.com/nf-core/sarek/pull/537) - Update workflow figure
 - [#539](https://github.com/nf-core/sarek/pull/539) - Update `CITATIONS.md`
+- [#544](https://github.com/nf-core/sarek/pull/544) - `Mutect2` is no longer compatible with `--no_intervals`
 
 ### Fixed
 
diff --git a/conf/modules.config b/conf/modules.config
index ddc3cad4d2..baf058e8cd 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -737,7 +737,8 @@ process{
     }
 
     //MUTECT2
-    withName: 'GATK4_CALCULATECONTAMINATION' {
+    withName: 'CALCULATECONTAMINATION' {
+        ext.args         = { "-tumor-segmentation ${meta.id}.segmentation.table" }
         publishDir        = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
@@ -747,7 +748,6 @@ process{
 
     withName: 'CONCAT_MUTECT2.*' {
         publishDir       = [
-            enabled: !params.no_intervals,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
             pattern: "*{vcf.gz,vcf.gz.tbi}"
@@ -763,20 +763,42 @@ process{
         ]
     }
 
-    withName: 'GATHERPILEUPSUMMARIES.*' {
-        ext.prefix       = { "${meta.id}.table" }
-        ext.when         = { "${!params.no_intervals}"}
+    withName: 'GATHERPILEUPSUMMARIES' {
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
+    withName: 'GATHERPILEUPSUMMARIES' {
         publishDir       = [
-            enabled: !params.no_intervals,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
+    withName: 'GATHERPILEUPSUMMARIES_.*' {
+        publishDir       = [
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
     withName: 'GETPILEUPSUMMARIES.*' {
         publishDir        = [
-            enabled: params.no_intervals,
+            mode: params.publish_dir_mode,
+            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
+            pattern: "*.table",
+            saveAs: { meta.num_intervals > 1 ? null : it }
+        ]
+    }
+
+    withName: 'LEARNREADORIENTATIONMODEL'{
+        ext.prefix       = { "${meta.id}.artifactprior" }
+        publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
@@ -784,7 +806,7 @@ process{
     }
 
     withName: 'MERGEMUTECTSTATS' {
-        ext.prefix       = { "${meta.id}.vcf.gz" }
+        ext.prefix       = { "${meta.id}" }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
@@ -794,12 +816,12 @@ process{
 
     withName: 'MUTECT2'{
         ext.when         = { params.tools && params.tools.contains('mutect2') }
-        ext.args         = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true" : "" }
+        ext.args         = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${meta.id}.f1r2.tar.gz" : "--f1r2-tar-gz ${meta.id}.f1r2.tar.gz" }
         publishDir       = [
-            enabled: params.no_intervals,
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
-            pattern: "*{gz,gz.tbi,stats}"
+            pattern: "*{vcf.gz,vcf.gz.tbi,stats}",
+            saveAs: { meta.num_intervals > 1 ? null : it }
         ]
     }
 
@@ -884,34 +906,11 @@ process{
     }
 
     //MUTECT2
-    withName: 'CALCULATECONTAMINATION' {
-        //ext.args         = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true" : "" }
-        publishDir       = [
-            mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
 
-    withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:GATHERPILEUPSUMMARIES.*' {
-        ext.prefix       = { "${meta.id}.table" }
-        publishDir       = [
-            enabled: !params.no_intervals,
-            mode: params.publish_dir_mode,
-            //use ${meta.tumor_id}_vs_${meta_normal_id} to publish in the same directory as the remainders of the
-            //somatic output whilst keeping the filename prefix identifiable for status type
-            path: { "${params.outdir}/variant_calling/${meta.tumor_id}_vs_${meta.normal_id}/mutect2" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
-    withName: 'LEARNREADORIENTATIONMODEL' {
-        ext.prefix         = { "${meta.id}.learnreadorientationmodel" }
-        publishDir       = [
-            mode: params.publish_dir_mode,
-            path: { "${params.outdir}/variant_calling/${meta.id}/mutect2" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
+    withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:MUTECT2' {
+        ext.args         = { params.ignore_soft_clipped_bases ?
+                            "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${meta.id}.f1r2.tar.gz --normal-sample ${meta.patient}_${meta.normal_id}" :
+                            "--f1r2-tar-gz ${meta.id}.f1r2.tar.gz --normal-sample ${meta.patient}_${meta.normal_id}" }
     }
 
     //MSISENSORPRO
diff --git a/modules.json b/modules.json
index d792373f86..2f80d79252 100644
--- a/modules.json
+++ b/modules.json
@@ -79,70 +79,70 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/applybqsr": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/applybqsrspark": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/applyvqsr": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/baserecalibrator": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/baserecalibratorspark": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "fd7ee6799abf1bd5228b4b59ce541f3aeaa2280b"
             },
             "gatk4/calculatecontamination": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/createsequencedictionary": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/estimatelibrarycomplexity": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/filtermutectcalls": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/gatherbqsrreports": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/gatherpileupsummaries": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/genomicsdbimport": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/genotypegvcfs": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/getpileupsummaries": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "f40cfefc0899fd6bb6adc300142ca6c3a35573ff"
             },
             "gatk4/haplotypecaller": {
-                "git_sha": "68f1c27169946f931ea4318911de5681f88b2961"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/intervallisttobed": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/learnreadorientationmodel": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/markduplicates": {
-                "git_sha": "0511e7fbbfa4ba41940d33b687b1cc90227b4eb8"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/markduplicatesspark": {
                 "git_sha": "e04970b7d249365cafa5a52912f9a28840481c05"
             },
             "gatk4/mergemutectstats": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/mutect2": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "gatk4/variantrecalibrator": {
-                "git_sha": "409af2f27cbe45109acc7fee70718d2bf20aa449"
+                "git_sha": "169b2b96c1167f89ab07127b7057c1d90a6996c7"
             },
             "manta/germline": {
                 "git_sha": "ffedf09b6e84b479c9c901274f74bb33f3777243"
@@ -172,7 +172,7 @@
                 "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
             },
             "samtools/bam2fq": {
-                "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+                "git_sha": "5510ea39fe638594bc26ac34cadf4a84bf27d159"
             },
             "samtools/collatefastq": {
                 "git_sha": "705f8c9ac4dfdf07666e71abde28f267e2dfd5eb"
@@ -196,7 +196,7 @@
                 "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
             },
             "samtools/view": {
-                "git_sha": "897c33d5da084b61109500ee44c01da2d3e4e773"
+                "git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
             },
             "seqkit/split2": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
diff --git a/modules/nf-core/modules/ascat/main.nf b/modules/nf-core/modules/ascat/main.nf
index 3b53bc0991..fc5b4315df 100644
--- a/modules/nf-core/modules/ascat/main.nf
+++ b/modules/nf-core/modules/ascat/main.nf
@@ -53,7 +53,7 @@ process ASCAT {
     ascat.prepareHTS(
         tumourseqfile = "$input_tumor",
         normalseqfile = "$input_normal",
-        tumourname = "Tumour",
+        tumourname = "meta.sample_id",
         normalname = "Normal",
         allelecounter_exe = "alleleCounter",
         alleles.prefix = "$allele_files",
diff --git a/modules/nf-core/modules/gatk4/applybqsr/main.nf b/modules/nf-core/modules/gatk4/applybqsr/main.nf
index 7a64dab252..a0e2c45ca0 100644
--- a/modules/nf-core/modules/gatk4/applybqsr/main.nf
+++ b/modules/nf-core/modules/gatk4/applybqsr/main.nf
@@ -2,10 +2,10 @@ process GATK4_APPLYBQSR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
diff --git a/modules/nf-core/modules/gatk4/applybqsrspark/main.nf b/modules/nf-core/modules/gatk4/applybqsrspark/main.nf
index 04303c09cd..9d7891ba1e 100644
--- a/modules/nf-core/modules/gatk4/applybqsrspark/main.nf
+++ b/modules/nf-core/modules/gatk4/applybqsrspark/main.nf
@@ -2,10 +2,10 @@ process GATK4_APPLYBQSR_SPARK {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
diff --git a/modules/nf-core/modules/gatk4/applyvqsr/main.nf b/modules/nf-core/modules/gatk4/applyvqsr/main.nf
index 8b2358093a..d3da833213 100644
--- a/modules/nf-core/modules/gatk4/applyvqsr/main.nf
+++ b/modules/nf-core/modules/gatk4/applyvqsr/main.nf
@@ -2,10 +2,10 @@ process GATK4_APPLYVQSR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches)
diff --git a/modules/nf-core/modules/gatk4/baserecalibrator/main.nf b/modules/nf-core/modules/gatk4/baserecalibrator/main.nf
index 766a833895..fb26d3da73 100644
--- a/modules/nf-core/modules/gatk4/baserecalibrator/main.nf
+++ b/modules/nf-core/modules/gatk4/baserecalibrator/main.nf
@@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)
diff --git a/modules/nf-core/modules/gatk4/baserecalibratorspark/main.nf b/modules/nf-core/modules/gatk4/baserecalibratorspark/main.nf
index 70c7018171..79988b72c3 100644
--- a/modules/nf-core/modules/gatk4/baserecalibratorspark/main.nf
+++ b/modules/nf-core/modules/gatk4/baserecalibratorspark/main.nf
@@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR_SPARK {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
-        'broadinstitute/gatk:4.2.3.0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)
diff --git a/modules/nf-core/modules/gatk4/calculatecontamination/main.nf b/modules/nf-core/modules/gatk4/calculatecontamination/main.nf
index 197fe6c2e8..c289684edb 100644
--- a/modules/nf-core/modules/gatk4/calculatecontamination/main.nf
+++ b/modules/nf-core/modules/gatk4/calculatecontamination/main.nf
@@ -2,10 +2,10 @@ process GATK4_CALCULATECONTAMINATION {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(pileup), path(matched)
diff --git a/modules/nf-core/modules/gatk4/createsequencedictionary/main.nf b/modules/nf-core/modules/gatk4/createsequencedictionary/main.nf
index dbf3704842..13fa9e8100 100644
--- a/modules/nf-core/modules/gatk4/createsequencedictionary/main.nf
+++ b/modules/nf-core/modules/gatk4/createsequencedictionary/main.nf
@@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY {
     tag "$fasta"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     path fasta
diff --git a/modules/nf-core/modules/gatk4/estimatelibrarycomplexity/main.nf b/modules/nf-core/modules/gatk4/estimatelibrarycomplexity/main.nf
index caa34630a0..46e09a95bb 100644
--- a/modules/nf-core/modules/gatk4/estimatelibrarycomplexity/main.nf
+++ b/modules/nf-core/modules/gatk4/estimatelibrarycomplexity/main.nf
@@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/modules/gatk4/filtermutectcalls/main.nf b/modules/nf-core/modules/gatk4/filtermutectcalls/main.nf
index c1c82e0b5f..91f6defa9a 100644
--- a/modules/nf-core/modules/gatk4/filtermutectcalls/main.nf
+++ b/modules/nf-core/modules/gatk4/filtermutectcalls/main.nf
@@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate)
diff --git a/modules/nf-core/modules/gatk4/gatherbqsrreports/main.nf b/modules/nf-core/modules/gatk4/gatherbqsrreports/main.nf
index 1f5f2e1bbc..231bd39e6a 100644
--- a/modules/nf-core/modules/gatk4/gatherbqsrreports/main.nf
+++ b/modules/nf-core/modules/gatk4/gatherbqsrreports/main.nf
@@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(table)
diff --git a/modules/nf-core/modules/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/modules/gatk4/gatherpileupsummaries/main.nf
index f5e9cf22a0..0b763f4169 100644
--- a/modules/nf-core/modules/gatk4/gatherpileupsummaries/main.nf
+++ b/modules/nf-core/modules/gatk4/gatherpileupsummaries/main.nf
@@ -2,10 +2,10 @@ process GATK4_GATHERPILEUPSUMMARIES {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
 
     input:
diff --git a/modules/nf-core/modules/gatk4/genomicsdbimport/main.nf b/modules/nf-core/modules/gatk4/genomicsdbimport/main.nf
index d2b78899ae..810f2b63b1 100644
--- a/modules/nf-core/modules/gatk4/genomicsdbimport/main.nf
+++ b/modules/nf-core/modules/gatk4/genomicsdbimport/main.nf
@@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace)
diff --git a/modules/nf-core/modules/gatk4/genotypegvcfs/main.nf b/modules/nf-core/modules/gatk4/genotypegvcfs/main.nf
index 0df88d662e..11024b1b23 100644
--- a/modules/nf-core/modules/gatk4/genotypegvcfs/main.nf
+++ b/modules/nf-core/modules/gatk4/genotypegvcfs/main.nf
@@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index)
diff --git a/modules/nf-core/modules/gatk4/getpileupsummaries/main.nf b/modules/nf-core/modules/gatk4/getpileupsummaries/main.nf
index c0946f7167..1c05617049 100644
--- a/modules/nf-core/modules/gatk4/getpileupsummaries/main.nf
+++ b/modules/nf-core/modules/gatk4/getpileupsummaries/main.nf
@@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(index), path(intervals)
@@ -40,7 +40,7 @@ process GATK4_GETPILEUPSUMMARIES {
         --variant $variants \\
         --output ${prefix}.pileups.table \\
         $reference_command \\
-        $sites_command \\
+        $interval_command \\
         --tmp-dir . \\
         $args
 
diff --git a/modules/nf-core/modules/gatk4/haplotypecaller/main.nf b/modules/nf-core/modules/gatk4/haplotypecaller/main.nf
index 2cd9e7d4e3..6dd3f69e48 100644
--- a/modules/nf-core/modules/gatk4/haplotypecaller/main.nf
+++ b/modules/nf-core/modules/gatk4/haplotypecaller/main.nf
@@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)
diff --git a/modules/nf-core/modules/gatk4/intervallisttobed/main.nf b/modules/nf-core/modules/gatk4/intervallisttobed/main.nf
index c0f9df635d..84f3c472ea 100644
--- a/modules/nf-core/modules/gatk4/intervallisttobed/main.nf
+++ b/modules/nf-core/modules/gatk4/intervallisttobed/main.nf
@@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOBED {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(intervals)
diff --git a/modules/nf-core/modules/gatk4/learnreadorientationmodel/main.nf b/modules/nf-core/modules/gatk4/learnreadorientationmodel/main.nf
index 717cf21122..8c4ac94e6f 100644
--- a/modules/nf-core/modules/gatk4/learnreadorientationmodel/main.nf
+++ b/modules/nf-core/modules/gatk4/learnreadorientationmodel/main.nf
@@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(f1r2)
diff --git a/modules/nf-core/modules/gatk4/markduplicates/main.nf b/modules/nf-core/modules/gatk4/markduplicates/main.nf
index 2650925b7b..97a8c3e1e4 100644
--- a/modules/nf-core/modules/gatk4/markduplicates/main.nf
+++ b/modules/nf-core/modules/gatk4/markduplicates/main.nf
@@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/modules/gatk4/mergemutectstats/main.nf b/modules/nf-core/modules/gatk4/mergemutectstats/main.nf
index 409e06f6a3..54311df7f5 100644
--- a/modules/nf-core/modules/gatk4/mergemutectstats/main.nf
+++ b/modules/nf-core/modules/gatk4/mergemutectstats/main.nf
@@ -2,10 +2,10 @@ process GATK4_MERGEMUTECTSTATS {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(stats)
diff --git a/modules/nf-core/modules/gatk4/mutect2/main.nf b/modules/nf-core/modules/gatk4/mutect2/main.nf
index 4a1f576880..abec0d73d3 100644
--- a/modules/nf-core/modules/gatk4/mutect2/main.nf
+++ b/modules/nf-core/modules/gatk4/mutect2/main.nf
@@ -2,10 +2,10 @@ process GATK4_MUTECT2 {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index), path(intervals)
@@ -57,4 +57,18 @@ process GATK4_MUTECT2 {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
+    touch ${prefix}.vcf.gz.stats
+    touch ${prefix}.f1r2.tar.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/modules/gatk4/variantrecalibrator/main.nf b/modules/nf-core/modules/gatk4/variantrecalibrator/main.nf
index cdcc1221f7..120aeade7a 100644
--- a/modules/nf-core/modules/gatk4/variantrecalibrator/main.nf
+++ b/modules/nf-core/modules/gatk4/variantrecalibrator/main.nf
@@ -2,10 +2,10 @@ process GATK4_VARIANTRECALIBRATOR {
     tag "$meta.id"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
diff --git a/modules/nf-core/modules/samtools/bam2fq/main.nf b/modules/nf-core/modules/samtools/bam2fq/main.nf
index 5d6aa79d46..9301d1d33c 100644
--- a/modules/nf-core/modules/samtools/bam2fq/main.nf
+++ b/modules/nf-core/modules/samtools/bam2fq/main.nf
@@ -45,7 +45,7 @@ process SAMTOOLS_BAM2FQ {
             bam2fq \\
             $args \\
             -@ $task.cpus \\
-            $inputbam >${prefix}_interleaved.fq.gz
+            $inputbam | gzip --no-name > ${prefix}_interleaved.fq.gz
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
diff --git a/modules/nf-core/modules/samtools/view/main.nf b/modules/nf-core/modules/samtools/view/main.nf
index 5f14fbbf2c..55194e887f 100644
--- a/modules/nf-core/modules/samtools/view/main.nf
+++ b/modules/nf-core/modules/samtools/view/main.nf
@@ -8,7 +8,7 @@ process SAMTOOLS_VIEW {
         'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
-    tuple val(meta), path(input)
+    tuple val(meta), path(input), path(index)
     path fasta
 
     output:
@@ -41,4 +41,16 @@ process SAMTOOLS_VIEW {
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+    touch ${prefix}.cram
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/modules/samtools/view/meta.yml b/modules/nf-core/modules/samtools/view/meta.yml
index 5604bfa7cd..a8b43ecce6 100644
--- a/modules/nf-core/modules/samtools/view/meta.yml
+++ b/modules/nf-core/modules/samtools/view/meta.yml
@@ -25,6 +25,10 @@ input:
       type: file
       description: BAM/CRAM/SAM file
       pattern: "*.{bam,cram,sam}"
+  - index:
+      type: optional file
+      description: BAM.BAI/CRAM.CRAI file
+      pattern: "*.{.bai,.crai}"
   - fasta:
       type: optional file
       description: Reference file the CRAM was created with
diff --git a/nextflow_schema.json b/nextflow_schema.json
index d72264c160..e5e029de25 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -57,14 +57,14 @@
                     "type": "string",
                     "fa_icon": "fas fa-toolbox",
                     "description": "Tools to use for variant calling and/or for annotation.",
-                    "help_text": "Multiple separated with commas.\n\nGermline variant calling can currently only be performed with the following variant callers:\n- FreeBayes, HaplotypeCaller, Manta, mpileup, Strelka, TIDDIT\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- ASCAT, Control-FREEC, FreeBayes, Manta, MSIsensorpro, Mutect2, Strelka\n\nTumor-only somatic variant calling can currently only be performed with the following variant callers:\n- Control-FREEC, Manta, mpileup, Mutect2, TIDDIT\n\nAnnotation is done using snpEff, VEP, or even both consecutively.\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted.\n\n\n\n`DNAseq`, `DNAscope` and `TNscope` are only available with `--sentieon`\n\n> **NB** tools can be specified with no concern for case.",
+                    "help_text": "Multiple separated with commas.\n\nGermline variant calling can currently only be performed with the following variant callers:\n- FreeBayes, HaplotypeCaller, Manta, mpileup, Strelka, TIDDIT\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- ASCAT, Control-FREEC, FreeBayes, Manta, MSIsensorpro, Mutect2, Strelka\n\n**NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\nTumor-only somatic variant calling can currently only be performed with the following variant callers:\n- Control-FREEC, Manta, mpileup, Mutect2, TIDDIT\n\nAnnotation is done using snpEff, VEP, or even both consecutively.\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted.\n\n\n\n`DNAseq`, `DNAscope` and `TNscope` are only available with `--sentieon`\n\n> **NB** tools can be specified with no concern for case.",
                     "pattern": "^((ascat|cnvkit|controlfreec|deepvariant|dnascope|dnaseq|freebayes|haplotypecaller|manta|merge|mpileup|msisensorpro|mutect2|snpeff|strelka|tiddit|tnscope|vep)*,?)*$"
                 },
                 "no_intervals": {
                     "type": "boolean",
                     "fa_icon": "fas fa-ban",
                     "description": "Disable usage of intervals.",
-                    "help_text": "Intervals are part of the genome chopped up, used to speed up preprocessing and variant calling."
+                    "help_text": "Intervals are part of the genome chopped up, used to speed up preprocessing and variant calling. Cannot be combined with `--tools mutect2`"
                 },
                 "nucleotides_per_second": {
                     "type": "number",
diff --git a/subworkflows/local/pair_variant_calling.nf b/subworkflows/local/pair_variant_calling.nf
index 41d21b6c24..72441bb89e 100644
--- a/subworkflows/local/pair_variant_calling.nf
+++ b/subworkflows/local/pair_variant_calling.nf
@@ -147,27 +147,26 @@ workflow PAIR_VARIANT_CALLING {
         msisensorpro_output = msisensorpro_output.mix(MSISENSORPRO_MSI_SOMATIC.out.output_report)
     }
 
-    // if (tools.contains('mutect2')) {
-    //     cram_pair_intervals.map{ meta, normal_cram, normal_crai, tumor_cram, tumor_crai, intervals ->
-    //             [meta, [normal_cram, tumor_cram], [normal_crai, tumor_crai], intervals, ['normal']]
-    //             }.set{cram_pair_mutect2}
-
-    //     GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING(
-    //         cram_pair_mutect2,
-    //         fasta,
-    //         fasta_fai,
-    //         dict,
-    //         germline_resource,
-    //         germline_resource_tbi,
-    //         panel_of_normals,
-    //         panel_of_normals_tbi,
-    //         intervals_bed_combine_gz,
-    //         num_intervals
-    //     )
-
-    //     mutect2_vcf = GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING.out.mutect2_vcf
-    //     ch_versions = ch_versions.mix(GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING.out.versions)
-    // }
+    if (tools.contains('mutect2')) {
+        cram_pair_mutect2 = cram_pair_intervals.map{ meta, normal_cram, normal_crai, tumor_cram, tumor_crai, intervals ->
+                                [meta, [normal_cram, tumor_cram], [normal_crai, tumor_crai], intervals]
+                            }
+
+        GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING(
+            cram_pair_mutect2,
+            fasta,
+            fasta_fai,
+            dict,
+            germline_resource,
+            germline_resource_tbi,
+            panel_of_normals,
+            panel_of_normals_tbi,
+            intervals_bed_combine_gz
+            )
+
+        mutect2_vcf = GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING.out.filtered_vcf
+        ch_versions = ch_versions.mix(GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING.out.versions)
+    }
 
     // if (tools.contains('tiddit')) {
     // }
diff --git a/subworkflows/local/tumor_variant_calling.nf b/subworkflows/local/tumor_variant_calling.nf
index c3ebcf1fb9..f382cb79d0 100644
--- a/subworkflows/local/tumor_variant_calling.nf
+++ b/subworkflows/local/tumor_variant_calling.nf
@@ -101,25 +101,20 @@ workflow TUMOR_ONLY_VARIANT_CALLING {
         ch_versions   = ch_versions.mix(RUN_FREEBAYES.out.versions)
     }
 
-    // if (tools.contains('mutect2')) {
-
-    //     which_norm = []
-    //     cram_recalibrated_intervals.map{ meta, cram, crai, intervals -> [meta, cram, crai, intervals, which_norm]}.set{cram_recalibrated_mutect2}
-    //     GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING(cram_recalibrated_mutect2,
-    //                                             fasta,
-    //                                             fasta_fai,
-    //                                             dict,
-    //                                             germline_resource,
-    //                                             germline_resource_tbi,
-    //                                             panel_of_normals,
-    //                                             panel_of_normals_tbi,
-    //                                             intervals_bed_combine_gz,
-    //                                             num_intervals)
-
-    //     mutect2_vcf = GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING.out.mutect2_vcf
-    //     ch_versions = ch_versions.mix(GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING.out.versions)
-
-    // }
+    if (tools.contains('mutect2')) {
+        GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING(cram_recalibrated_intervals,
+                                                fasta,
+                                                fasta_fai,
+                                                dict,
+                                                germline_resource,
+                                                germline_resource_tbi,
+                                                panel_of_normals,
+                                                panel_of_normals_tbi,
+                                                intervals_bed_combine_gz)
+
+        mutect2_vcf = GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING.out.filtered_vcf
+        ch_versions = ch_versions.mix(GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING.out.versions)
+    }
 
     if (tools.contains('manta')){
         RUN_MANTA_TUMORONLY(cram_recalibrated_intervals_gz_tbi,
diff --git a/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf b/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf
index 1d6620df4d..19e4a37350 100644
--- a/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf
+++ b/subworkflows/nf-core/gatk4/tumor_normal_somatic_variant_calling/main.nf
@@ -2,17 +2,17 @@
 // Run GATK mutect2 in tumor normal mode, getepileupsummaries, calculatecontamination, learnreadorientationmodel and filtermutectcalls
 //
 
-include { TABIX_BGZIP                     as BGZIP_MUTECT2               } from '../../../../modules/nf-core/modules/tabix/bgzip/main'
+include { TABIX_BGZIP                     as BGZIP_VC_MUTECT2            } from '../../../../modules/nf-core/modules/tabix/bgzip/main'
 include { CONCAT_VCF                      as CONCAT_MUTECT2              } from '../../../../modules/local/concat_vcf/main'
-include { GATK4_MUTECT2                   as MUTECT2                     } from '../../../../modules/nf-core/modules/gatk4/mutect2/main'
-include { GATK4_MERGEMUTECTSTATS          as MERGEMUTECTSTATS            } from '../../../../modules/nf-core/modules/gatk4/mergemutectstats/main'
-include { GATK4_LEARNREADORIENTATIONMODEL as LEARNREADORIENTATIONMODEL   } from '../../../../modules/nf-core/modules/gatk4/learnreadorientationmodel/main'
-include { GATK4_GATHERPILEUPSUMMARIES     as GATHERPILEUPSUMMARIES_TUMOR } from '../../../../modules/nf-core/modules/gatk4/gatherpileupsummaries/main'
-include { GATK4_GATHERPILEUPSUMMARIES     as GATHERPILEUPSUMMARIES_NORMAL} from '../../../../modules/nf-core/modules/gatk4/gatherpileupsummaries/main'
-include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_TUMOR    } from '../../../../modules/nf-core/modules/gatk4/getpileupsummaries/main'
-include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_NORMAL   } from '../../../../modules/nf-core/modules/gatk4/getpileupsummaries/main'
 include { GATK4_CALCULATECONTAMINATION    as CALCULATECONTAMINATION      } from '../../../../modules/nf-core/modules/gatk4/calculatecontamination/main'
 include { GATK4_FILTERMUTECTCALLS         as FILTERMUTECTCALLS           } from '../../../../modules/nf-core/modules/gatk4/filtermutectcalls/main'
+include { GATK4_GATHERPILEUPSUMMARIES     as GATHERPILEUPSUMMARIES_NORMAL} from '../../../../modules/nf-core/modules/gatk4/gatherpileupsummaries/main'
+include { GATK4_GATHERPILEUPSUMMARIES     as GATHERPILEUPSUMMARIES_TUMOR } from '../../../../modules/nf-core/modules/gatk4/gatherpileupsummaries/main'
+include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_NORMAL   } from '../../../../modules/nf-core/modules/gatk4/getpileupsummaries/main'
+include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES_TUMOR    } from '../../../../modules/nf-core/modules/gatk4/getpileupsummaries/main'
+include { GATK4_LEARNREADORIENTATIONMODEL as LEARNREADORIENTATIONMODEL   } from '../../../../modules/nf-core/modules/gatk4/learnreadorientationmodel/main'
+include { GATK4_MERGEMUTECTSTATS          as MERGEMUTECTSTATS            } from '../../../../modules/nf-core/modules/gatk4/mergemutectstats/main'
+include { GATK4_MUTECT2                   as MUTECT2                     } from '../../../../modules/nf-core/modules/gatk4/mutect2/main'
 
 workflow GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING {
     take:
@@ -24,8 +24,7 @@ workflow GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING {
     germline_resource_tbi     // channel: /path/to/germline/index
     panel_of_normals          // channel: /path/to/panel/of/normals
     panel_of_normals_tbi      // channel: /path/to/panel/of/normals/index
-    intervals_bed_combine_gz
-    num_intervals
+    intervals_bed_combine_gz  // Combined intervals file for merging!
 
     main:
     ch_versions = Channel.empty()
@@ -33,141 +32,198 @@ workflow GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING {
     //
     //Perform variant calling using mutect2 module in tumor single mode.
     //
-    MUTECT2 ( input, false, false, false, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
-    ch_versions = ch_versions.mix(MUTECT2.out.versions)
-
-    //
-    //Generate pileup summary tables using getepileupsummaries. tumor sample should always be passed in as the first input and input list entries of ch_mutect2_in,
-    //to ensure correct file order for calculatecontamination.
-    input.multiMap{  meta, input_list, input_index_list, intervals, which_norm ->
-        tumor: [ meta, input_list[1], input_index_list[1], intervals ]
-        normal: [ meta, input_list[0], input_index_list[0], intervals ]
-    }.set{pileup}
-
-    GETPILEUPSUMMARIES_TUMOR ( pileup.tumor, fasta, fai, dict, germline_resource, germline_resource_tbi )
-    GETPILEUPSUMMARIES_NORMAL ( pileup.normal, fasta, fai, dict, germline_resource, germline_resource_tbi )
-    ch_versions = ch_versions.mix(GETPILEUPSUMMARIES_NORMAL.out.versions)
+    MUTECT2(input,
+            fasta,
+            fai,
+            dict,
+            germline_resource,
+            germline_resource_tbi,
+            panel_of_normals,
+            panel_of_normals_tbi)
 
     // Figure out if using intervals or no_intervals
     MUTECT2.out.vcf.branch{
-            intervals:    num_intervals > 1
-            no_intervals: num_intervals == 1
-        }.set{ mutect2_vcf }
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
+        }.set{ mutect2_vcf_branch }
 
     MUTECT2.out.tbi.branch{
-            intervals:    num_intervals > 1
-            no_intervals: num_intervals == 1
-        }.set{ mutect2_tbi }
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
+        }.set{ mutect2_tbi_branch }
 
     MUTECT2.out.stats.branch{
-            intervals:    num_intervals > 1
-            no_intervals: num_intervals == 1
-        }.set{ mutect2_stats }
-
-    GETPILEUPSUMMARIES_NORMAL.out.table.branch{
-            intervals:    num_intervals > 1
-            no_intervals: num_intervals == 1
-        }set{ pileup_table_normal }
-
-    GETPILEUPSUMMARIES_TUMOR.out.table.branch{
-            intervals:    num_intervals > 1
-            no_intervals: num_intervals == 1
-        }set{ pileup_table_tumor }
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
+        }.set{ mutect2_stats_branch }
 
+    MUTECT2.out.f1r2.branch{
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
+        }.set{ mutect2_f1r2_branch }
 
     //Only when using intervals
-
     //Merge Mutect2 VCF
-    BGZIP_MUTECT2(MUTECT2.out.vcf)
+    BGZIP_VC_MUTECT2(mutect2_vcf_branch.intervals)
 
     CONCAT_MUTECT2(
-        BGZIP_MUTECT2.out.output.map{ meta, vcf ->
-            [[id: meta.tumor_id + "_vs_" + meta.normal_id, normal_id: meta.normal_id, tumor_id: meta.tumor_id, gender: meta.gender, patient: meta.patient ], vcf]
-        }.groupTuple(size: num_intervals),
+        BGZIP_VC_MUTECT2.out.output
+        .map{ meta, vcf ->
+            new_meta = meta.clone()
+            new_meta.id = new_meta.tumor_id + "_vs_" + new_meta.normal_id
+
+            def groupKey = groupKey(meta, meta.num_intervals)
+            [new_meta, vcf]
+        }.groupTuple(),
         fai,
         intervals_bed_combine_gz)
 
     mutect2_vcf = Channel.empty().mix(
         CONCAT_MUTECT2.out.vcf,
-        mutect2_vcf.no_intervals)
+        mutect2_vcf_branch.no_intervals)
 
     mutect2_tbi = Channel.empty().mix(
         CONCAT_MUTECT2.out.tbi,
-        mutect2_tbi.no_intervals)
-
-    ch_versions = ch_versions.mix(BGZIP_MUTECT2.out.versions)
-    ch_versions = ch_versions.mix(CONCAT_MUTECT2.out.versions)
+        mutect2_tbi_branch.no_intervals)
 
     //Merge Muteect2 Stats
-    MERGEMUTECTSTATS(mutect2_stats.intervals.map{ meta, stats ->
-        [[id: meta.tumor_id + "_vs_" + meta.normal_id, normal_id: meta.normal_id, tumor_id: meta.tumor_id, gender: meta.gender, patient: meta.patient ], stats]
-    }.groupTuple(size: num_intervals))
+    MERGEMUTECTSTATS(
+        mutect2_stats_branch.intervals
+        .map{ meta, stats ->
+            new_meta = meta.clone()
+            new_meta.id = new_meta.tumor_id + "_vs_" + new_meta.normal_id
+
+            def groupKey = groupKey(meta, meta.num_intervals)
+            [new_meta, stats]
+        }.groupTuple())
 
     mutect2_stats = Channel.empty().mix(
         MERGEMUTECTSTATS.out.stats,
-        mutect2_stats.no_intervals)
+        mutect2_stats_branch.no_intervals)
+
+    //
+    //Generate artifactpriors using learnreadorientationmodel on the f1r2 output of mutect2.
+    //
+    LEARNREADORIENTATIONMODEL(
+        mutect2_f1r2_branch.intervals
+            .map{ meta, f1r2 ->
+                new_meta = meta.clone()
+                new_meta.id = new_meta.tumor_id + "_vs_" + new_meta.normal_id
+
+                def groupKey = groupKey(meta, meta.num_intervals)
+                [new_meta, f1r2]
+            }.groupTuple())
+
+    //
+    //Generate pileup summary tables using getepileupsummaries. tumor sample should always be passed in as the first input and input list entries of ch_mutect2_in,
+    //to ensure correct file order for calculatecontamination.
+    pileup = input.multiMap{  meta, input_list, input_index_list, intervals ->
+        tumor: [ meta, input_list[1], input_index_list[1], intervals ]
+        normal: [ meta, input_list[0], input_index_list[0], intervals ]
+    }
+
+    GETPILEUPSUMMARIES_TUMOR ( pileup.tumor.map{
+                                    meta, cram, crai, intervals ->
+                                    new_meta = meta.clone()
+                                    new_meta.id = new_meta.num_intervals <= 1 ? new_meta.tumor_id : new_meta.tumor_id + "_" + intervals.baseName
+                                    [new_meta, cram, crai, intervals]
+                                },
+                                fasta, fai, dict, germline_resource, germline_resource_tbi )
+
+    GETPILEUPSUMMARIES_NORMAL ( pileup.normal.map{
+                                    meta, cram, crai, intervals ->
+                                    new_meta = meta.clone()
+                                    new_meta.id = new_meta.num_intervals <= 1 ? new_meta.normal_id : new_meta.normal_id + "_" + intervals.baseName
+                                    [new_meta, cram, crai, intervals]
+                                },
+                                fasta, fai, dict, germline_resource, germline_resource_tbi )
+
+    GETPILEUPSUMMARIES_NORMAL.out.table.branch{
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
+        }set{ pileup_table_normal }
+
+    GETPILEUPSUMMARIES_TUMOR.out.table.branch{
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
+        }set{ pileup_table_tumor }
 
     //Merge Pileup Summaries
     GATHERPILEUPSUMMARIES_NORMAL(
-        GETPILEUPSUMMARIES_NORMAL.out.table.map{ meta, table ->
-            [[id: meta.normal_id, normal_id: meta.normal_id, tumor_id: meta.tumor_id, gender: meta.gender, patient: meta.patient ], table]
-        }.groupTuple(size: num_intervals),
+        GETPILEUPSUMMARIES_NORMAL.out.table
+        .map{ meta, table ->
+            new_meta = meta.clone()
+            new_meta.id = new_meta.normal_id
+
+            def groupKey = groupKey(meta, meta.num_intervals)
+            [new_meta, table]
+        }.groupTuple(),
         dict)
 
     gather_table_normal = Channel.empty().mix(
-        GATHERPILEUPSUMMARIES_NORMAL.out.table.map{ meta, table ->
-            [[id: meta.tumor_id + "_vs_" + meta.normal_id, normal_id: meta.normal_id, tumor_id: meta.tumor_id, gender: meta.gender, patient: meta.patient ], table]
-        },
-        pileup_table_normal.no_intervals)
-
-    GATHERPILEUPSUMMARIES_TUMOR( GETPILEUPSUMMARIES_TUMOR.out.table.map{ meta, table ->
-            [[id: meta.tumor_id, normal_id: meta.normal_id, tumor_id: meta.tumor_id, gender: meta.gender, patient: meta.patient ], table]
-        }.groupTuple(size: num_intervals),
+        GATHERPILEUPSUMMARIES_NORMAL.out.table,
+        pileup_table_normal.no_intervals).map{ meta, table ->
+            new_meta = meta.clone()
+            new_meta.id = new_meta.tumor_id + "_vs_" + new_meta.normal_id
+            [new_meta, table]
+        }
+
+    GATHERPILEUPSUMMARIES_TUMOR(
+        GETPILEUPSUMMARIES_TUMOR.out.table
+        .map{ meta, table ->
+            new_meta = meta.clone()
+            new_meta.id = new_meta.tumor_id
+
+            def groupKey = groupKey(meta, meta.num_intervals)
+            [new_meta, table]
+        }.groupTuple(),
         dict)
 
     gather_table_tumor = Channel.empty().mix(
-        GATHERPILEUPSUMMARIES_TUMOR.out.table.map{ meta, table ->
-            [[id: meta.tumor_id + "_vs_" + meta.normal_id, normal_id: meta.normal_id, tumor_id: meta.tumor_id, gender: meta.gender, patient: meta.patient ], table]
-        },
-        pileup_table_tumor.no_intervals)
-
-    //
-    //Generate artifactpriors using learnreadorientationmodel on the f1r2 output of mutect2.
-    //
-    MUTECT2.out.f1r2.map{ meta, f1f2 ->
-        [[id: meta.tumor_id + "_vs_" + meta.normal_id, normal_id: meta.normal_id, tumor_id: meta.tumor_id, gender: meta.gender, patient: meta.patient ], f1f2]
-    }.groupTuple(size: num_intervals)
-    .set{ch_learnread_in}
-
-    LEARNREADORIENTATIONMODEL (ch_learnread_in)
-    ch_versions = ch_versions.mix(LEARNREADORIENTATIONMODEL.out.versions)
+        GATHERPILEUPSUMMARIES_TUMOR.out.table,
+        pileup_table_tumor.no_intervals).map{ meta, table ->
+            new_meta = meta.clone()
+            new_meta.id = new_meta.tumor_id + "_vs_" + new_meta.normal_id
+            [new_meta, table]
+        }
 
     //
     //Contamination and segmentation tables created using calculatecontamination on the pileup summary table.
     //
-    ch_calccon_in       = gather_table_tumor.join(gather_table_normal)
-    CALCULATECONTAMINATION ( ch_calccon_in, true )
-    ch_versions   = ch_versions.mix(CALCULATECONTAMINATION.out.versions)
+    CALCULATECONTAMINATION ( gather_table_tumor.join(gather_table_normal) )
 
     //
     //Mutect2 calls filtered by filtermutectcalls using the artifactpriors, contamination and segmentation tables.
     //
+    mutect2_vcf.view()
+    mutect2_tbi.view()
+    LEARNREADORIENTATIONMODEL.out.artifactprior.view()
+    CALCULATECONTAMINATION.out.segmentation.view()
+    CALCULATECONTAMINATION.out.contamination.view()
     ch_filtermutect    = mutect2_vcf.join(mutect2_tbi)
                                     .join(mutect2_stats)
                                     .join(LEARNREADORIENTATIONMODEL.out.artifactprior)
                                     .join(CALCULATECONTAMINATION.out.segmentation)
                                     .join(CALCULATECONTAMINATION.out.contamination)
-    ch_filtermutect.map{ meta, vcf, tbi, stats, orientation, seg, cont ->
-        [meta, vcf, tbi, stats, orientation, seg, cont, []]
-    }.set{ch_filtermutect_in}
+    ch_filtermutect_in = ch_filtermutect.map{ meta, vcf, tbi, stats, orientation, seg, cont -> [meta, vcf, tbi, stats, orientation, seg, cont, []] }
 
     FILTERMUTECTCALLS ( ch_filtermutect_in, fasta, fai, dict )
-    ch_versions              = ch_versions.mix(FILTERMUTECTCALLS.out.versions)
+
+    ch_versions = ch_versions.mix(BGZIP_VC_MUTECT2.out.versions)
+    ch_versions = ch_versions.mix(CONCAT_MUTECT2.out.versions)
+    ch_versions = ch_versions.mix(CALCULATECONTAMINATION.out.versions)
+    ch_versions = ch_versions.mix(FILTERMUTECTCALLS.out.versions)
+    ch_versions = ch_versions.mix(GETPILEUPSUMMARIES_NORMAL.out.versions)
+    ch_versions = ch_versions.mix(GETPILEUPSUMMARIES_TUMOR.out.versions)
+    ch_versions = ch_versions.mix(GATHERPILEUPSUMMARIES_NORMAL.out.versions)
+    ch_versions = ch_versions.mix(GATHERPILEUPSUMMARIES_TUMOR.out.versions)
+    ch_versions = ch_versions.mix(LEARNREADORIENTATIONMODEL.out.versions)
+    ch_versions = ch_versions.mix(MERGEMUTECTSTATS.out.versions)
+    ch_versions = ch_versions.mix(MUTECT2.out.versions)
 
     emit:
     mutect2_vcf            = mutect2_vcf                                    // channel: [ val(meta), [ vcf ] ]
     mutect2_stats          = mutect2_stats                                  // channel: [ val(meta), [ stats ] ]
-    mutect2_f1r2           = MUTECT2.out.f1r2                               // channel: [ val(meta), [ f1r2 ] ]
 
     artifact_priors        = LEARNREADORIENTATIONMODEL.out.artifactprior    // channel: [ val(meta), [ artifactprior ] ]
 
@@ -177,7 +233,9 @@ workflow GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING {
     contamination_table    = CALCULATECONTAMINATION.out.contamination       // channel: [ val(meta), [ contamination ] ]
     segmentation_table     = CALCULATECONTAMINATION.out.segmentation        // channel: [ val(meta), [ segmentation ] ]
 
-    filtered_vcf           = FILTERMUTECTCALLS.out.vcf                      // channel: [ val(meta), [ vcf ] ]
+    filtered_vcf           = FILTERMUTECTCALLS.out.vcf.map{ meta, vcf ->
+                                            meta.variantcaller = "Mutect2"
+                                            [meta, vcf]}                      // channel: [ val(meta), [ vcf ] ]
     filtered_tbi           = FILTERMUTECTCALLS.out.tbi                      // channel: [ val(meta), [ tbi ] ]
     filtered_stats         = FILTERMUTECTCALLS.out.stats                    // channel: [ val(meta), [ stats ] ]
 
diff --git a/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf b/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf
index 6e94218d23..6b8ccf1da1 100644
--- a/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf
+++ b/subworkflows/nf-core/gatk4/tumor_only_somatic_variant_calling/main.nf
@@ -2,14 +2,15 @@
 // Run GATK mutect2 in tumor only mode, getepileupsummaries, calculatecontamination and filtermutectcalls
 //
 
-include { TABIX_BGZIP                  as BGZIP_VC_MUTECT2       } from '../../../../modules/nf-core/modules/tabix/bgzip/main'
-include { CONCAT_VCF                   as CONCAT_MUTECT2         } from '../../../../modules/local/concat_vcf/main'
-include { GATK4_MUTECT2                as MUTECT2                } from '../../../../modules/nf-core/modules/gatk4/mutect2/main'
-include { GATK4_MERGEMUTECTSTATS       as MERGEMUTECTSTATS       } from '../../../../modules/nf-core/modules/gatk4/mergemutectstats/main'
-include { GATK4_GETPILEUPSUMMARIES     as GETPILEUPSUMMARIES     } from '../../../../modules/nf-core/modules/gatk4/getpileupsummaries/main'
-include { GATK4_GATHERPILEUPSUMMARIES  as GATHERPILEUPSUMMARIES  } from '../../../../modules/nf-core/modules/gatk4/gatherpileupsummaries/main'
-include { GATK4_CALCULATECONTAMINATION as CALCULATECONTAMINATION } from '../../../../modules/nf-core/modules/gatk4/calculatecontamination/main'
-include { GATK4_FILTERMUTECTCALLS      as FILTERMUTECTCALLS      } from '../../../../modules/nf-core/modules/gatk4/filtermutectcalls/main'
+include { TABIX_BGZIP                     as BGZIP_VC_MUTECT2          } from '../../../../modules/nf-core/modules/tabix/bgzip/main'
+include { CONCAT_VCF                      as CONCAT_MUTECT2            } from '../../../../modules/local/concat_vcf/main'
+include { GATK4_CALCULATECONTAMINATION    as CALCULATECONTAMINATION    } from '../../../../modules/nf-core/modules/gatk4/calculatecontamination/main'
+include { GATK4_FILTERMUTECTCALLS         as FILTERMUTECTCALLS         } from '../../../../modules/nf-core/modules/gatk4/filtermutectcalls/main'
+include { GATK4_GETPILEUPSUMMARIES        as GETPILEUPSUMMARIES        } from '../../../../modules/nf-core/modules/gatk4/getpileupsummaries/main'
+include { GATK4_GATHERPILEUPSUMMARIES     as GATHERPILEUPSUMMARIES     } from '../../../../modules/nf-core/modules/gatk4/gatherpileupsummaries/main'
+include { GATK4_LEARNREADORIENTATIONMODEL as LEARNREADORIENTATIONMODEL } from '../../../../modules/nf-core/modules/gatk4/learnreadorientationmodel/main'
+include { GATK4_MERGEMUTECTSTATS          as MERGEMUTECTSTATS          } from '../../../../modules/nf-core/modules/gatk4/mergemutectstats/main'
+include { GATK4_MUTECT2                   as MUTECT2                   } from '../../../../modules/nf-core/modules/gatk4/mutect2/main'
 
 workflow GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING {
     take:
@@ -21,8 +22,7 @@ workflow GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING {
     germline_resource_tbi     // channel: /path/to/germline/index
     panel_of_normals          // channel: /path/to/panel/of/normals
     panel_of_normals_tbi      // channel: /path/to/panel/of/normals/index
-    intervals_bed_combine_gz
-    num_intervals
+    intervals_bed_combine_gz  // Combined intervals file for merging!
 
     main:
     ch_versions = Channel.empty()
@@ -30,47 +30,49 @@ workflow GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING {
     //
     //Perform variant calling using mutect2 module in tumor single mode.
     //
-    MUTECT2 ( input , true , false , false , fasta , fai , dict , germline_resource , germline_resource_tbi , panel_of_normals , panel_of_normals_tbi )
-
-    //
-    //Generate pileup summary table using getepileupsummaries.
-    //
-    pileup_input = input.map {
-        meta, input_file, input_index, intervals, which_norm ->
-        [meta, input_file, input_index, intervals]
-    }
-    GETPILEUPSUMMARIES ( pileup_input , fasta, fai, dict, germline_resource , germline_resource_tbi )
+    MUTECT2(input,
+            fasta,
+            fai,
+            dict,
+            germline_resource,
+            germline_resource_tbi,
+            panel_of_normals,
+            panel_of_normals_tbi)
 
     // Figure out if using intervals or no_intervals
     MUTECT2.out.vcf.branch{
-            intervals:    num_intervals > 1
-            no_intervals: num_intervals == 1
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
         }.set{ mutect2_vcf_branch }
 
     MUTECT2.out.tbi.branch{
-            intervals:    num_intervals > 1
-            no_intervals: num_intervals == 1
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
         }.set{ mutect2_tbi_branch }
 
     MUTECT2.out.stats.branch{
-            intervals:    num_intervals > 1
-            no_intervals: num_intervals == 1
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
         }.set{ mutect2_stats_branch }
 
-    GETPILEUPSUMMARIES.out.table.branch{
-            intervals:    num_intervals > 1
-            no_intervals: num_intervals == 1
-        }set{ pileup_table_branch }
+    MUTECT2.out.f1r2.branch{
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
+        }.set{ mutect2_f1r2_branch }
 
     //Only when using intervals
     //Merge Mutect2 VCF
     BGZIP_VC_MUTECT2(mutect2_vcf_branch.intervals)
 
-    CONCAT_MUTECT2(BGZIP_VC_MUTECT2.out.output.map{ meta, vcf ->
+    CONCAT_MUTECT2(
+        BGZIP_VC_MUTECT2.out.output
+        .map{ meta, vcf ->
             new_meta = meta.clone()
             new_meta.id = new_meta.sample
+
+            def groupKey = groupKey(meta, meta.num_intervals)
             [new_meta, vcf]
-        }.groupTuple(size: num_intervals),
+        }.groupTuple(),
         fai,
         intervals_bed_combine_gz)
 
@@ -82,23 +84,56 @@ workflow GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING {
         CONCAT_MUTECT2.out.tbi,
         mutect2_tbi_branch.no_intervals)
 
-    //Merge Muteect2 Stats
-    MERGEMUTECTSTATS(mutect2_stats_branch.intervals.map{ meta, stats ->
-        new_meta = meta.clone()
-        new_meta.id = new_meta.sample
-        [new_meta, stats]
-    }.groupTuple(size: num_intervals))
+    //Merge Mutect2 Stats
+    MERGEMUTECTSTATS(
+        mutect2_stats_branch.intervals
+        .map{ meta, stats ->
+            new_meta = meta.clone()
+            new_meta.id = new_meta.sample
+
+            def groupKey = groupKey(meta, meta.num_intervals)
+            [new_meta, stats]
+        }.groupTuple())
 
     mutect2_stats = Channel.empty().mix(
         MERGEMUTECTSTATS.out.stats,
         mutect2_stats_branch.no_intervals)
 
+    //
+    //Generate artifactpriors using learnreadorientationmodel on the f1r2 output of mutect2.
+    //
+    LEARNREADORIENTATIONMODEL(
+        Channel.empty().mix(
+            mutect2_f1r2_branch.intervals
+            .map{ meta, f1r2 ->
+                new_meta = meta.clone()
+                new_meta.id = new_meta.sample
+
+                def groupKey = groupKey(meta, meta.num_intervals)
+                [new_meta, f1r2]
+            }.groupTuple(),
+            mutect2_f1r2_branch.no_intervals))
+
+    //
+    //Generate pileup summary table using getepileupsummaries.
+    //
+    GETPILEUPSUMMARIES ( input , fasta, fai, dict, germline_resource , germline_resource_tbi )
+
+    GETPILEUPSUMMARIES.out.table.branch{
+            intervals:    it[0].num_intervals > 1
+            no_intervals: it[0].num_intervals <= 1
+        }set{ pileup_table_branch }
+
     //Merge Pileup Summaries
-    GATHERPILEUPSUMMARIES( GETPILEUPSUMMARIES.out.table.map{ meta, table ->
+    GATHERPILEUPSUMMARIES(
+        GETPILEUPSUMMARIES.out.table
+        .map{ meta, table ->
             new_meta = meta.clone()
             new_meta.id = new_meta.sample
+
+            def groupKey = groupKey(meta, meta.num_intervals)
             [new_meta, table]
-        }.groupTuple(size: num_intervals),
+        }.groupTuple(),
         dict)
 
     pileup_table = Channel.empty().mix(
@@ -108,26 +143,28 @@ workflow GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING {
     //
     //Contamination and segmentation tables created using calculatecontamination on the pileup summary table.
     //
-    pileup_table.map{meta, table -> [meta, table, []]}.set{table_contamination}
-    CALCULATECONTAMINATION ( table_contamination, true )
+    table_contamination = pileup_table.map{meta, table -> [meta, table, []]}
+    CALCULATECONTAMINATION ( table_contamination )
 
     //
     //Mutect2 calls filtered by filtermutectcalls using the contamination and segmentation tables.
     //
     ch_filtermutect    = mutect2_vcf.join(mutect2_tbi)
                                     .join(mutect2_stats)
+                                    .join(LEARNREADORIENTATIONMODEL.out.artifactprior)
                                     .join(CALCULATECONTAMINATION.out.segmentation)
                                     .join(CALCULATECONTAMINATION.out.contamination)
-    ch_filtermutect_in = ch_filtermutect.map{ meta, vcf, tbi, stats, seg, cont -> [meta, vcf, tbi, stats, [], seg, cont, []] }
+    ch_filtermutect_in = ch_filtermutect.map{ meta, vcf, tbi, stats, artifactprior, seg, cont -> [meta, vcf, tbi, stats, artifactprior, seg, cont, []] }
 
     FILTERMUTECTCALLS ( ch_filtermutect_in, fasta, fai, dict )
 
     ch_versions = ch_versions.mix(BGZIP_VC_MUTECT2.out.versions)
-    ch_versions = ch_versions.mix(CALCULATECONTAMINATION.out.versions)
     ch_versions = ch_versions.mix(CONCAT_MUTECT2.out.versions)
+    ch_versions = ch_versions.mix(CALCULATECONTAMINATION.out.versions)
     ch_versions = ch_versions.mix(FILTERMUTECTCALLS.out.versions)
-    ch_versions = ch_versions.mix(GATHERPILEUPSUMMARIES.out.versions)
     ch_versions = ch_versions.mix(GETPILEUPSUMMARIES.out.versions)
+    ch_versions = ch_versions.mix(GATHERPILEUPSUMMARIES.out.versions)
+    ch_versions = ch_versions.mix(LEARNREADORIENTATIONMODEL.out.versions)
     ch_versions = ch_versions.mix(MERGEMUTECTSTATS.out.versions)
     ch_versions = ch_versions.mix(MUTECT2.out.versions)
 
@@ -135,12 +172,16 @@ workflow GATK_TUMOR_ONLY_SOMATIC_VARIANT_CALLING {
     mutect2_vcf         = mutect2_vcf                               // channel: [ val(meta), [ vcf ] ]
     mutect2_stats       = mutect2_stats                              // channel: [ val(meta), [ stats ] ]
 
+    artifact_priors     = LEARNREADORIENTATIONMODEL.out.artifactprior    // channel: [ val(meta), [ artifactprior ] ]
+
     pileup_table        = pileup_table                              // channel: [ val(meta), [ table ] ]
 
     contamination_table = CALCULATECONTAMINATION.out.contamination  // channel: [ val(meta), [ contamination ] ]
     segmentation_table  = CALCULATECONTAMINATION.out.segmentation   // channel: [ val(meta), [ segmentation ] ]
 
-    filtered_vcf        = FILTERMUTECTCALLS.out.vcf                 // channel: [ val(meta), [ vcf ] ]
+    filtered_vcf        = FILTERMUTECTCALLS.out.vcf.map{ meta, vcf ->
+                                            meta.variantcaller = "Mutect2"
+                                        [meta, vcf] }                 // channel: [ val(meta), [ vcf ] ]
     filtered_index      = FILTERMUTECTCALLS.out.tbi                 // channel: [ val(meta), [ tbi ] ]
     filtered_stats      = FILTERMUTECTCALLS.out.stats               // channel: [ val(meta), [ stats ] ]
 
diff --git a/tests/nextflow.config b/tests/nextflow.config
index ca18d021f9..571a04f5a0 100644
--- a/tests/nextflow.config
+++ b/tests/nextflow.config
@@ -22,4 +22,9 @@ process {
         }
     }
 
+    withName: 'NFCORE_SAREK:SAREK:PAIR_VARIANT_CALLING:GATK_TUMOR_NORMAL_SOMATIC_VARIANT_CALLING:MUTECT2'{
+        //sample name from when the test data was generated
+        ext.args = { "--f1r2-tar-gz ${meta.id}.f1r2.tar.gz --normal-sample normal " }
+    }
+
 }
diff --git a/tests/test_tools.yml b/tests/test_tools.yml
index 38a4efacb4..b7f5e451ab 100644
--- a/tests/test_tools.yml
+++ b/tests/test_tools.yml
@@ -298,7 +298,8 @@
     - 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.table.pileupsummaries.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
@@ -310,19 +311,13 @@
     - no_intervals
     - 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.pileups.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
+  exit_code: 1
+  stdout:
+    contains:
+      - "--tools mutect2 and --no_intervals cannot be used together."
 
 - name: Run variant calling on somatic sample with mutect2
-  command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2
+  command: nextflow run main.nf -profile test,tools_somatic,docker --tools mutect2 -c ./tests/nextflow.config
   tags:
     - mutect2
     - somatic
@@ -333,9 +328,9 @@
     - 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.table.pileupsummaries.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.table.pileupsummaries.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.learnreadorientationmodel.tar.gz
+    - 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
@@ -347,18 +342,10 @@
     - no_intervals
     - 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.pileups.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4.pileups.table
-    - path: results/variant_calling/sample4_vs_sample3/mutect2/sample4_vs_sample3.learnreadorientationmodel.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
+  exit_code: 1
+  stdout:
+    contains:
+      - "--tools mutect2 and --no_intervals cannot be used together."
 
 - name: Run variant calling on somatic sample with msisensor-pro
   command: nextflow run main.nf -profile test,tools_somatic,docker --tools msisensorpro
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index 68ce35299c..b763d45926 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -69,6 +69,11 @@ if (params.wes) {
     if (params.intervals && !params.intervals.endsWith("bed") && !params.intervals.endsWith("interval_list")) exit 1, "Interval file must end with .bed or .interval_list"
 }
 
+
+if(params.tools && params.tools.contains('mutect2') && params.no_intervals){
+    log.error "--tools mutect2 and --no_intervals cannot be used together.\nOne of the tools within the Mutect2 subworkflow requires intervals. They can be provided to the pipeline with --intervals. If none are provided, they will be generated from the FASTA file.\nFor more information on the Mutect2 workflow, see here: https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2.\nFor more information on GetPileupsummaries, see here: https://gatk.broadinstitute.org/hc/en-us/articles/5358860217115-GetPileupSummaries"
+    exit 1
+}
 // Save AWS IGenomes file containing annotation version
 def anno_readme = params.genomes[params.genome]?.readme
 if (anno_readme && file(anno_readme).exists()) {
@@ -965,7 +970,7 @@ def extract_csv(csv_file) {
             def fastq_1     = file(row.fastq_1, checkIfExists: true)
             def fastq_2     = file(row.fastq_2, checkIfExists: true)
             def CN          = params.seq_center ? "CN:${params.seq_center}\\t" : ''
-            def read_group  = "\"@RG\\tID:${row.lane}\\t${CN}PU:${row.lane}\\tSM:${row.sample}\\tLB:${row.sample}\\tPL:${params.seq_platform}\""
+            def read_group  = "\"@RG\\tID:${row.lane}\\t${CN}PU:${row.lane}\\tSM:${row.patient}_${row.sample}\\tLB:${row.sample}\\tDS:${params.fasta}\\tPL:${params.seq_platform}\""
             meta.numLanes   = numLanes.toInteger()
             meta.read_group = read_group.toString()
             meta.data_type  = "fastq"