diff --git a/CHANGELOG.md b/CHANGELOG.md
index daada653d5..1a51757c48 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - [#1339](https://github.com/nf-core/sarek/pull/1339) - Update sentieon-modules
+- [#1344](https://github.com/nf-core/sarek/pull/1344) - Enable CRAM QC, when starting from variantcalling
 
 ### Fixed
 
diff --git a/conf/modules/modules.config b/conf/modules/modules.config
index a0411793a6..f24cb481b7 100644
--- a/conf/modules/modules.config
+++ b/conf/modules/modules.config
@@ -78,12 +78,12 @@ process {
         ]
     }
 
-    if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')))) {
-        withName: 'NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH' {
+    if (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator'))) {
+        withName: 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:MOSDEPTH' {
             ext.prefix = { "${meta.id}.recal" }
         }
 
-        withName: 'NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS' {
+        withName: 'NFCORE_SAREK:SAREK:CRAM_SAMPLEQC:CRAM_QC_RECAL:SAMTOOLS_STATS' {
             ext.prefix = { "${meta.id}.recal.cram" }
             ext.when   = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) }
             publishDir = [
diff --git a/docs/images/sarek_subway.png b/docs/images/sarek_subway.png
index ff73d272d9..02937f57e5 100644
Binary files a/docs/images/sarek_subway.png and b/docs/images/sarek_subway.png differ
diff --git a/docs/images/sarek_subway.svg b/docs/images/sarek_subway.svg
index d6d1653c12..2a7831b02b 100644
--- a/docs/images/sarek_subway.svg
+++ b/docs/images/sarek_subway.svg
@@ -8,7 +8,7 @@
    version="1.1"
    id="svg5"
    inkscape:version="1.3 (0e150ed, 2023-07-21)"
-   sodipodi:docname="sarek_subway.svg"
+   sodipodi:docname="sarek_subway(2).svg"
    inkscape:export-filename="sarek_subway.png"
    inkscape:export-xdpi="600"
    inkscape:export-ydpi="600"
@@ -33,13 +33,13 @@
      inkscape:document-units="mm"
      showgrid="false"
      inkscape:zoom="1.4142136"
-     inkscape:cx="521.49124"
-     inkscape:cy="291.68154"
-     inkscape:window-width="2544"
-     inkscape:window-height="826"
-     inkscape:window-x="12"
-     inkscape:window-y="37"
-     inkscape:window-maximized="0"
+     inkscape:cx="521.84479"
+     inkscape:cy="348.60363"
+     inkscape:window-width="2560"
+     inkscape:window-height="1027"
+     inkscape:window-x="0"
+     inkscape:window-y="25"
+     inkscape:window-maximized="1"
      inkscape:current-layer="layer4"
      width="211mm"
      fit-margin-top="0"
@@ -52,7 +52,7 @@
      inkscape:deskcolor="#d1d1d1"
      showguides="false"
      inkscape:clip-to-page="false"
-     inkscape:export-bgcolor="#ffffff00"><inkscape:grid
+     inkscape:export-bgcolor="#ffffffff"><inkscape:grid
        type="xygrid"
        id="grid1459"
        originx="25.146553"
@@ -67,7 +67,10 @@
        height="220.24503"
        id="page1"
        margin="500mm 500mm 500mm 16.263456"
-       bleed="0" /></sodipodi:namedview><defs
+       bleed="0"
+       inkscape:export-filename="sarek_subway.png"
+       inkscape:export-xdpi="600"
+       inkscape:export-ydpi="600" /></sodipodi:namedview><defs
      id="defs2"><linearGradient
        id="linearGradient7169"
        inkscape:swatch="solid"><stop
@@ -745,9 +748,9 @@
          ry="9.3751783"
          rx="10.636381"
          y="-641.33673"
-         x="665.29053"
+         x="685.17792"
          height="225.00444"
-         width="149.51534"
+         width="129.62796"
          id="rect6693-7"
          style="display:inline;fill:#e6e6e6;fill-opacity:1;stroke:none;stroke-width:4.00201;stroke-linecap:butt;stroke-linejoin:bevel;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;paint-order:normal" /><rect
          ry="9.3751783"
@@ -763,7 +766,7 @@
          y="-641.33673"
          x="52.618313"
          height="225.00443"
-         width="569.12909"
+         width="536.64636"
          id="rect6693-4"
          style="display:inline;fill:#e6e6e6;fill-opacity:1;stroke:none;stroke-width:4.00201;stroke-linecap:butt;stroke-linejoin:bevel;stroke-miterlimit:4;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1;paint-order:normal" /><rect
          ry="9.3751783"
@@ -1272,20 +1275,6 @@
            x="555.26233"
            y="-36.968044"
            style="stroke-width:0.937508">mosdepth, samtools</tspan></text><text
-         xml:space="preserve"
-         style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:12.5px;line-height:1.25;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';display:inline;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.937508"
-         x="727.77972"
-         y="71.877167"
-         id="text714"
-         inkscape:export-filename="./polygon4618.png"
-         inkscape:export-xdpi="90"
-         inkscape:export-ydpi="90"
-         transform="rotate(-45)"><tspan
-           id="tspan712"
-           sodipodi:role="line"
-           x="727.77972"
-           y="71.877167"
-           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:12.5px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';text-align:center;text-anchor:middle;stroke-width:0.937508">mosdepth, samtools</tspan></text><text
          transform="rotate(-45)"
          inkscape:export-ydpi="90"
          inkscape:export-xdpi="90"
@@ -1305,15 +1294,22 @@
          inkscape:export-xdpi="90"
          inkscape:export-filename="./polygon4618.png"
          id="text751-3"
-         y="126.17035"
-         x="801.64581"
+         y="121.38352"
+         x="779.91632"
          style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:12.5px;line-height:1.25;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';display:inline;fill:#000000;fill-opacity:1;stroke:none;stroke-width:0.937508"
          xml:space="preserve"><tspan
            style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:12.5px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';text-align:center;text-anchor:middle;stroke-width:0.937508"
-           y="126.17035"
-           x="801.64581"
+           y="121.38352"
+           x="779.91632"
+           sodipodi:role="line"
+           id="tspan1"
+           dx="0 0.66291916">mosdepth, samtools</tspan><tspan
+           style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:12.5px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro';text-align:center;text-anchor:middle;stroke-width:0.937508"
+           y="137.00851"
+           x="779.91632"
            sodipodi:role="line"
-           id="tspan749-8">ngscheckmate</tspan></text><text
+           dx="0 0 0 0 0 0 0 0 0 0 0 0 0 0.66291916"
+           id="tspan2">ngscheckmate</tspan></text><text
          transform="rotate(-45)"
          inkscape:export-ydpi="90"
          inkscape:export-xdpi="90"
@@ -1465,7 +1461,7 @@
          d="m 534.2059,-568.59483 v 3.75 h -0.002 l 4.68933,4.85596 4.6875,-4.85596 v -3.75 z"
          id="path3215-2" /><g
          id="g3217-5-0"
-         transform="translate(12.495814,-1.8750371)"
+         transform="translate(-13.754186,-1.8750371)"
          style="display:inline;stroke-width:1.00002"><g
            id="g3211-1-2"
            transform="translate(535.08304)"
@@ -1811,12 +1807,6 @@
          style="display:inline;fill:#ffffff;fill-rule:evenodd;stroke:#000000;stroke-width:3.54334;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
          transform="scale(1,-1)" /><circle
          r="9.375"
-         cy="527.2608"
-         cx="604.49341"
-         id="circle1664-11"
-         style="display:inline;fill:#ffffff;fill-rule:evenodd;stroke:#000000;stroke-width:3.54379;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
-         transform="scale(1,-1)" /><circle
-         r="9.375"
          cy="527.26086"
          cx="763.96918"
          id="circle1664-34"
@@ -1824,7 +1814,7 @@
          transform="scale(1,-1)" /><circle
          r="9.375"
          cy="527.26105"
-         cx="681.04193"
+         cx="662.29193"
          id="circle1664-34-8"
          style="display:inline;fill:#ffffff;fill-rule:evenodd;stroke:#000000;stroke-width:3.54334;stroke-miterlimit:4;stroke-dasharray:none;stroke-opacity:1"
          transform="scale(1,-1)" /><circle
diff --git a/subworkflows/local/cram_sampleqc/main.nf b/subworkflows/local/cram_sampleqc/main.nf
index 3e3b06f008..f00e18aafe 100644
--- a/subworkflows/local/cram_sampleqc/main.nf
+++ b/subworkflows/local/cram_sampleqc/main.nf
@@ -1,15 +1,32 @@
-include { BAM_NGSCHECKMATE } from '../../../subworkflows/nf-core/bam_ngscheckmate/main'
-
+include { BAM_NGSCHECKMATE                           } from '../../../subworkflows/nf-core/bam_ngscheckmate/main'
+include { CRAM_QC_MOSDEPTH_SAMTOOLS as CRAM_QC_RECAL } from '../../../subworkflows/local/cram_qc_mosdepth_samtools/main'
 workflow CRAM_SAMPLEQC {
 
     take:
-    ch_cram             // channel: [ val(meta), cram, crai ]
-    ngscheckmate_bed    // channel: [ ngscheckmate_bed ]
-    fasta               // channel: [ fasta ]
+    ch_cram                     // channel: [ val(meta), cram, crai ]
+    ngscheckmate_bed            // channel: [ ngscheckmate_bed ]
+    fasta                       // channel: [ fasta ]
+    skip_baserecalibration      // boolean:
+    intervals_for_preprocessing // channel:
 
     main:
 
     ch_versions = Channel.empty()
+    reports     = Channel.empty()
+
+    if(!skip_baserecalibration){
+
+        CRAM_QC_RECAL(
+            ch_cram,
+            fasta,
+            intervals_for_preprocessing)
+
+        // Gather QC reports
+        reports = CRAM_QC_RECAL.out.reports.collect{ meta, report -> report }
+
+        // Gather used softwares versions
+        ch_versions = ch_versions.mix(CRAM_QC_RECAL.out.versions)
+    }
 
     ch_ngscheckmate_bed = ngscheckmate_bed.map{bed -> [[id: "ngscheckmate"], bed]}
 
@@ -24,6 +41,7 @@ workflow CRAM_SAMPLEQC {
     all          = BAM_NGSCHECKMATE.out.all          // channel: [ meta, all ]
     vcf          = BAM_NGSCHECKMATE.out.vcf          // channel: [ meta, vcf ]
     pdf          = BAM_NGSCHECKMATE.out.pdf          // channel: [ meta, pdf ]
+    reports
 
     versions = ch_versions                     // channel: [ versions.yml ]
 }
diff --git a/tests/test_cnvkit.yml b/tests/test_cnvkit.yml
index 3a1b8181cb..8e9017c70b 100644
--- a/tests/test_cnvkit.yml
+++ b/tests/test_cnvkit.yml
@@ -57,6 +57,30 @@
       md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
     - path: results/cnvkit
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on tumor_only sample with cnvkit
   command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools cnvkit --outdir results
   tags:
@@ -88,6 +112,17 @@
       md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
     - path: results/cnvkit
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
 - name: Run variant calling on germline sample with cnvkit
   command: nextflow run main.nf -profile test_cache,tools_germline --tools cnvkit --outdir results
   tags:
@@ -121,6 +156,17 @@
       md5sum: 79aae7e9c135fb8c65f8fbda12610faf
     - path: results/cnvkit
       should_exist: false
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
 - name: Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal
   command: nextflow run main.nf -profile test_cache,tools_somatic --tools cnvkit --only_paired_variant_calling --outdir results
   tags:
@@ -156,3 +202,27 @@
       md5sum: d15bf5061d90c8edbcba04d2bd2a270c
     - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
       md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
diff --git a/tests/test_controlfreec.yml b/tests/test_controlfreec.yml
index 32393aa501..dad942b50e 100644
--- a/tests/test_controlfreec.yml
+++ b/tests/test_controlfreec.yml
@@ -52,6 +52,30 @@
       should_exist: false
     - path: results/cnvkit
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on somatic samples with controlfreec without intervals
   command: nextflow run main.nf -profile test_cache,tools_somatic --tools controlfreec --no_intervals -stub-run --outdir results
   tags:
@@ -105,6 +129,26 @@
       should_exist: false
     - path: results/mpileup
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.global.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample3/sample3.recal.summary.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.global.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample4/sample4.recal.summary.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on tumor_only sample with controlfreec
   command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools controlfreec -stub-run --outdir results
   tags:
@@ -148,3 +192,14 @@
       should_exist: false
     - path: results/mpileup
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.global.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample2/sample2.recal.region.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample2/sample2.recal.summary.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
diff --git a/tests/test_deepvariant.yml b/tests/test_deepvariant.yml
index ce378e1e76..b91ad01fa2 100644
--- a/tests/test_deepvariant.yml
+++ b/tests/test_deepvariant.yml
@@ -24,6 +24,17 @@
     # binary changes md5sums on reruns
     - path: results/deepvariant
       should_exist: false
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
 - name: Run variant calling on germline sample with deepvariant without intervals
   command: nextflow run main.nf -profile test_cache,tools_germline --tools deepvariant --no_intervals --outdir results
   tags:
@@ -57,3 +68,12 @@
     # binary changes md5sums on reruns
     - path: results/deepvariant
       should_exist: false
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: d2775eb102acc5950f7f53883dcb503d
+    - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz
+      md5sum: 54431f155c9538809e8caf99d1a75ec7
+    - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi
+      md5sum: c67dcd711b096eb42f43784d5eadbc0d
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
diff --git a/tests/test_haplotypecaller.yml b/tests/test_haplotypecaller.yml
index 4ec225367b..85c06d5e75 100644
--- a/tests/test_haplotypecaller.yml
+++ b/tests/test_haplotypecaller.yml
@@ -34,6 +34,18 @@
     # binary changes md5sums on reruns
     - path: results/haplotypecaller
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/test/test.recal.cram.stats
+
 - name: Run variant calling on germline sample with haplotypecaller without intervals
   command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --no_intervals --outdir results
   tags:
@@ -77,3 +89,12 @@
     # binary changes md5sums on reruns
     - path: results/haplotypecaller
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_haplotypecaller_skip_filter.yml b/tests/test_haplotypecaller_skip_filter.yml
index def69fbbf3..8600485d33 100644
--- a/tests/test_haplotypecaller_skip_filter.yml
+++ b/tests/test_haplotypecaller_skip_filter.yml
@@ -38,6 +38,17 @@
       should_exist: false
     - path: results/haplotypecaller
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/test/test.recal.cram.stats
 - name: Run variant calling on germline sample with haplotypecaller without intervals and skip filter
   command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --skip_tools haplotypecaller_filter --no_intervals --outdir results
   tags:
@@ -81,3 +92,12 @@
       should_exist: false
     - path: results/haplotypecaller
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_joint_germline.yml b/tests/test_joint_germline.yml
index 6bd7b4532f..7b634193c6 100644
--- a/tests/test_joint_germline.yml
+++ b/tests/test_joint_germline.yml
@@ -30,7 +30,28 @@
     - path: results/variant_calling/haplotypecaller/testT/testT.haplotypecaller.g.vcf.gz.tbi
     - path: results/haplotypecaller
       should_exist: false
-
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/testN/testN.recal.cram.stats
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt
+      md5sum: ba97ed85645f77da6f3adad138b3cdb4
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt
+      md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt
+      md5sum: a937108cbf24c1430b79c861234ce22b
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
+      md5sum: d2b579a74bf8d858f82869f073056252
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/testT/testT.recal.cram.stats
 - name: Run joint germline variant calling with haplotypecaller all intervals at once
   command: nextflow run main.nf -profile test_cache,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results --nucleotides_per_second 100
   tags:
@@ -63,7 +84,28 @@
     - path: results/variant_calling/haplotypecaller/testT/testT.haplotypecaller.g.vcf.gz.tbi
     - path: results/haplotypecaller
       should_exist: false
-
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/testN/testN.recal.cram.stats
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt
+      md5sum: ba97ed85645f77da6f3adad138b3cdb4
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt
+      md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt
+      md5sum: a937108cbf24c1430b79c861234ce22b
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
+      md5sum: d2b579a74bf8d858f82869f073056252
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/testT/testT.recal.cram.stats
 - name: Run joint germline variant calling with haplotypecaller with Stub for VQSR
   command: nextflow run main.nf -profile test_cache,tools_germline --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results -stub-run
   tags:
@@ -101,3 +143,25 @@
     - path: results/variant_calling/haplotypecaller/testT/testT.haplotypecaller.g.vcf.gz.tbi
     - path: results/haplotypecaller
       should_exist: false
+    - path: results/reports/mosdepth/testN/testN.recal.global.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testN/testN.recal.region.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testN/testN.recal.summary.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/samtools/testN/testN.recal.cram.stats
+    - path: results/reports/mosdepth/testT/testT.recal.global.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testT/testT.recal.region.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testT/testT.recal.summary.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/samtools/testT/testT.recal.cram.stats
diff --git a/tests/test_manta.yml b/tests/test_manta.yml
index 1e53587f6e..b119ca80b7 100644
--- a/tests/test_manta.yml
+++ b/tests/test_manta.yml
@@ -22,6 +22,17 @@
     # binary changes md5sums on reruns
     - path: results/manta
       should_exist: false
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
 - name: Run variant calling on germline sample with manta without intervals
   command: nextflow run main.nf -profile test_cache,tools_germline --tools manta --no_intervals --outdir results
   tags:
@@ -53,6 +64,15 @@
       md5sum: 4cb176febbc8c26d717a6c6e67b9c905
     - path: results/manta
       should_exist: false
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: d2775eb102acc5950f7f53883dcb503d
+    - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz
+      md5sum: 54431f155c9538809e8caf99d1a75ec7
+    - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi
+      md5sum: c67dcd711b096eb42f43784d5eadbc0d
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
 - name: Run variant calling on tumor_only sample with manta
   command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools manta --outdir results
   tags:
@@ -77,6 +97,17 @@
       md5sum: 4cb176febbc8c26d717a6c6e67b9c905
     - path: results/manta
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
 - name: Run variant calling on tumor_only sample with manta without intervals
   command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools manta --no_intervals --outdir results
   tags:
@@ -108,6 +139,15 @@
       md5sum: 4cb176febbc8c26d717a6c6e67b9c905
     - path: results/manta
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 0a7300e56eda6fba7c7564f00aa000f0
+    - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz
+      md5sum: 3de4a9f4da2f2b4909ef192452a8d211
+    - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi
+      md5sum: cfb07b0ba46e8468b4342edb243536f3
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
 - name: Run variant calling on somatic sample with manta
   command: nextflow run main.nf -profile test_cache,tools_somatic --tools manta --outdir results
   tags:
@@ -156,6 +196,30 @@
       md5sum: 4cb176febbc8c26d717a6c6e67b9c905
     - path: results/manta
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on somatic sample with manta without intervals
   command: nextflow run main.nf -profile test_cache,tools_somatic --tools manta --no_intervals --outdir results
   tags:
@@ -211,3 +275,23 @@
       md5sum: 4cb176febbc8c26d717a6c6e67b9c905
     - path: results/manta
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: d2775eb102acc5950f7f53883dcb503d
+    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz
+      md5sum: 54431f155c9538809e8caf99d1a75ec7
+    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi
+      md5sum: c67dcd711b096eb42f43784d5eadbc0d
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 0a7300e56eda6fba7c7564f00aa000f0
+    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz
+      md5sum: 3de4a9f4da2f2b4909ef192452a8d211
+    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi
+      md5sum: cfb07b0ba46e8468b4342edb243536f3
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
diff --git a/tests/test_mpileup.yml b/tests/test_mpileup.yml
index 7cff9dad23..f7c5d87749 100644
--- a/tests/test_mpileup.yml
+++ b/tests/test_mpileup.yml
@@ -13,6 +13,17 @@
       should_exist: false
     - path: results/mpileup
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
 - name: Run variant calling on tumor_only sample to test mpileup without intervals
   command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools mpileup --no_intervals --outdir results
   tags:
@@ -35,6 +46,15 @@
       should_exist: false
     - path: results/mpileup
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 0a7300e56eda6fba7c7564f00aa000f0
+    - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz
+      md5sum: 3de4a9f4da2f2b4909ef192452a8d211
+    - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi
+      md5sum: cfb07b0ba46e8468b4342edb243536f3
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
 - name: Run variant calling on germline sample to test mpileup
   command: nextflow run main.nf -profile test_cache,tools_germline --tools mpileup --outdir results
   tags:
@@ -50,6 +70,17 @@
       should_exist: false
     - path: results/mpileup
       should_exist: false
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
 - name: Run variant calling on germline sample to test mpileup without intervals
   command: nextflow run main.nf -profile test_cache,tools_germline --tools mpileup --no_intervals --outdir results
   tags:
@@ -72,3 +103,12 @@
       should_exist: false
     - path: results/mpileup
       should_exist: false
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: d2775eb102acc5950f7f53883dcb503d
+    - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz
+      md5sum: 54431f155c9538809e8caf99d1a75ec7
+    - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi
+      md5sum: c67dcd711b096eb42f43784d5eadbc0d
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
diff --git a/tests/test_msisensorpro.yml b/tests/test_msisensorpro.yml
index 700187e0a4..173dbcf5ca 100644
--- a/tests/test_msisensorpro.yml
+++ b/tests/test_msisensorpro.yml
@@ -12,6 +12,30 @@
     - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_somatic
     - path: results/msisensorpro
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Build only index with msisensorpro
   command: nextflow run main.nf -profile test_cache --build_only_index --tools msisensorpro --input false --outdir results
   tags:
diff --git a/tests/test_mutect2.yml b/tests/test_mutect2.yml
index 0329e827d3..3ff6307485 100644
--- a/tests/test_mutect2.yml
+++ b/tests/test_mutect2.yml
@@ -38,6 +38,17 @@
     # binary changes md5sums on reruns
     - path: results/mutect2
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
 - name: Run variant calling on tumor only sample with mutect2 without intervals
   command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools mutect2 --no_intervals --outdir results
   tags:
@@ -85,3 +96,12 @@
     # binary changes md5sums on reruns
     - path: results/mutect2
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 0a7300e56eda6fba7c7564f00aa000f0
+    - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz
+      md5sum: 3de4a9f4da2f2b4909ef192452a8d211
+    - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi
+      md5sum: cfb07b0ba46e8468b4342edb243536f3
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
diff --git a/tests/test_sentieon_dnascope.yml b/tests/test_sentieon_dnascope.yml
index 946bed2d4f..babd1bef0d 100644
--- a/tests/test_sentieon_dnascope.yml
+++ b/tests/test_sentieon_dnascope.yml
@@ -34,6 +34,17 @@
     # binary changes md5sums on reruns
     - path: results/dnascope
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/test/test.recal.cram.stats
 - name: Run variant calling on germline sample with sentieons dnascope without intervals
   command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --no_intervals --outdir results
   tags:
@@ -77,6 +88,16 @@
     # binary changes md5sums on reruns
     - path: results/sentieon_dnascope
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: results/reports/samtools/test/test.recal.cram.stats
+
 - name: Run variant calling on germline sample with sentieons dnascope output gvcf
   command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode gvcf
   tags:
@@ -115,6 +136,17 @@
       should_exist: false
     - path: results/dnascope
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/test/test.recal.cram.stats
 - name: Run variant calling on germline sample with sentieons dnascope output both gvcf and vcf
   command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode variant,gvcf
   tags:
@@ -145,3 +177,14 @@
     - path: results/variant_calling/sentieon_dnascope/test/test.dnascope.unfiltered.vcf.gz.tbi
     - path: results/dnascope
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_sentieon_dnascope_joint_germline.yml b/tests/test_sentieon_dnascope_joint_germline.yml
index 234e657270..295bb45e7e 100644
--- a/tests/test_sentieon_dnascope_joint_germline.yml
+++ b/tests/test_sentieon_dnascope_joint_germline.yml
@@ -38,6 +38,28 @@
       should_exist: false
     - path: results/variant_calling/sentieon_dnascope/joint_variant_calling/joint_germline_recalibrated.vcf.gz.tbi
       should_exist: false
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/testN/testN.recal.cram.stats
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/testT/testT.recal.cram.stats
 - name: Run joint germline variant calling with sentieon dnascope all intervals at once
   command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_dnascope --step variant_calling --joint_germline --outdir results --sentieon_dnascope_emit_mode gvcf --nucleotides_per_second 100
   tags:
@@ -64,3 +86,25 @@
     - path: results/variant_calling/sentieon_dnascope/testT/testT.dnascope.g.vcf.gz.tbi
     - path: results/dnascope
       should_exist: false
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/testN/testN.recal.cram.stats
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/testT/testT.recal.cram.stats
diff --git a/tests/test_sentieon_dnascope_skip_filter.yml b/tests/test_sentieon_dnascope_skip_filter.yml
index 6906b7d04e..bd2a49b551 100644
--- a/tests/test_sentieon_dnascope_skip_filter.yml
+++ b/tests/test_sentieon_dnascope_skip_filter.yml
@@ -31,6 +31,17 @@
     # binary changes md5sums on reruns
     - path: results/sentieon_dnascope
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/test/test.recal.cram.stats
 - name: Run variant calling on germline sample with sentieon dnascope without intervals and skip filter
   command: nextflow run main.nf -profile test_cache,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --no_intervals --outdir results
   tags:
@@ -71,3 +82,12 @@
     # binary changes md5sums on reruns
     - path: results/sentieon_dnascope
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_sentieon_haplotyper.yml b/tests/test_sentieon_haplotyper.yml
index 7cac6f34c7..6567804259 100644
--- a/tests/test_sentieon_haplotyper.yml
+++ b/tests/test_sentieon_haplotyper.yml
@@ -34,6 +34,17 @@
     # binary changes md5sums on reruns
     - path: results/haplotyper
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/test/test.recal.cram.stats
 - name: Run variant calling on germline sample with sentieons haplotyper without intervals
   command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --no_intervals --outdir results
   tags:
@@ -77,6 +88,15 @@
     # binary changes md5sums on reruns
     - path: results/sentieon_haplotyper
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: results/reports/samtools/test/test.recal.cram.stats
 - name: Run variant calling on germline sample with sentieons haplotyper output gvcf
   command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode gvcf
   tags:
@@ -115,6 +135,17 @@
       should_exist: false
     - path: results/haplotyper
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/test/test.recal.cram.stats
 - name: Run variant calling on germline sample with sentieons haplotyper output both gvcf and vcf
   command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode variant,gvcf
   tags:
@@ -145,6 +176,17 @@
     - path: results/variant_calling/sentieon_haplotyper/test/test.haplotyper.unfiltered.vcf.gz.tbi
     - path: results/haplotyper
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/test/test.recal.cram.stats
 - name: Run variant calling on germline sample with sentieons haplotyper and gatk haplotypecaller
   command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller,sentieon_haplotyper --step variant_calling --outdir results
   tags:
@@ -189,3 +231,14 @@
     # binary changes md5sums on reruns
     - path: results/haplotyper
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_sentieon_haplotyper_joint_germline.yml b/tests/test_sentieon_haplotyper_joint_germline.yml
index 1c12f101db..3474764886 100644
--- a/tests/test_sentieon_haplotyper_joint_germline.yml
+++ b/tests/test_sentieon_haplotyper_joint_germline.yml
@@ -27,6 +27,28 @@
     - path: results/variant_calling/sentieon_haplotyper/testT/testT.haplotyper.g.vcf.gz.tbi
     - path: results/haplotyper
       should_exist: false
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/testN/testN.recal.cram.stats
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt
+      md5sum: ba97ed85645f77da6f3adad138b3cdb4
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt
+      md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt
+      md5sum: a937108cbf24c1430b79c861234ce22b
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
+      md5sum: d2b579a74bf8d858f82869f073056252
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/testT/testT.recal.cram.stats
 - name: Run joint germline variant calling with sentieon haplotyper all intervals at once
   command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf --nucleotides_per_second 100
   tags:
@@ -54,6 +76,28 @@
     - path: results/variant_calling/sentieon_haplotyper/testT/testT.haplotyper.g.vcf.gz.tbi
     - path: results/haplotyper
       should_exist: false
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt
+      md5sum: 3a2030e5e8af7bc12720c3a5592bf921
+    - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt
+      md5sum: 615c5c5019d88045a9ff5bbe6e63d270
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
+      md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/testN/testN.recal.cram.stats
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt
+      md5sum: ba97ed85645f77da6f3adad138b3cdb4
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt
+      md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b
+    - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt
+      md5sum: a937108cbf24c1430b79c861234ce22b
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
+      md5sum: d2b579a74bf8d858f82869f073056252
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
+      md5sum: 5c00a1d457c387d6e71848a6d897e309
+    - path: results/reports/samtools/testT/testT.recal.cram.stats
 - name: Run joint germline variant calling with sentieon haplotyper with stub for VQSR
   command: nextflow run main.nf -profile test_cache,software_license,tools_germline --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf -stub-run
   tags:
@@ -83,3 +127,25 @@
     - path: results/variant_calling/sentieon_haplotyper/testT/testT.haplotyper.g.vcf.gz.tbi
     - path: results/haplotyper
       should_exist: false
+    - path: results/reports/mosdepth/testN/testN.recal.global.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testN/testN.recal.region.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testN/testN.recal.summary.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/samtools/testN/testN.recal.cram.stats
+    - path: results/reports/mosdepth/testT/testT.recal.global.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testT/testT.recal.region.dist.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testT/testT.recal.summary.txt
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: results/reports/samtools/testT/testT.recal.cram.stats
diff --git a/tests/test_sentieon_haplotyper_skip_filter.yml b/tests/test_sentieon_haplotyper_skip_filter.yml
index b4229da7b4..f333f41558 100644
--- a/tests/test_sentieon_haplotyper_skip_filter.yml
+++ b/tests/test_sentieon_haplotyper_skip_filter.yml
@@ -35,6 +35,15 @@
     # binary changes md5sums on reruns
     - path: results/sentieon_haplotyper
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: results/reports/samtools/test/test.recal.cram.stats
 - name: Run variant calling on germline sample with sentieon haplotyper without intervals and skip filter
   command: nextflow run main.nf -profile test_cache,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --no_intervals --outdir results
   tags:
@@ -79,3 +88,12 @@
     # binary changes md5sums on reruns
     - path: results/sentieon_haplotyper
       should_exist: false
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt
+      md5sum: e82e90c7d508a135b5a8a7cd6933452e
+    - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt
+      md5sum: 4f0d231060cbde4efdd673863bd2fb59
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz
+      md5sum: bc1df47d46f818fee5275975925d769a
+    - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi
+      md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
+    - path: results/reports/samtools/test/test.recal.cram.stats
diff --git a/tests/test_strelka.yml b/tests/test_strelka.yml
index 2a3a24c936..766d9e18c7 100644
--- a/tests/test_strelka.yml
+++ b/tests/test_strelka.yml
@@ -76,6 +76,52 @@
       should_exist: false
     - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi
       should_exist: false
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on germline sample with strelka
   command: nextflow run main.nf -profile test_cache,tools_germline --tools strelka --outdir results
   tags:
@@ -104,6 +150,17 @@
     # binary changes md5sums on reruns
     - path: results/strelka
       should_exist: false
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
 - name: Run variant calling on germline sample with strelka without intervals
   command: nextflow run main.nf -profile test_cache,tools_germline --tools strelka --no_intervals --outdir results
   tags:
@@ -139,6 +196,15 @@
     # binary changes md5sums on reruns
     - path: results/strelka
       should_exist: false
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: d2775eb102acc5950f7f53883dcb503d
+    - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz
+      md5sum: 54431f155c9538809e8caf99d1a75ec7
+    - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi
+      md5sum: c67dcd711b096eb42f43784d5eadbc0d
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
 - name: Run variant calling on tumor only sample with strelka
   command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools strelka --outdir results
   tags:
@@ -167,6 +233,17 @@
     # binary changes md5sums on reruns
     - path: results/strelka
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
 - name: Run variant calling on tumor only sample with strelka without intervals
   command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools strelka --no_intervals --outdir results
   tags:
@@ -202,6 +279,15 @@
     # binary changes md5sums on reruns
     - path: results/strelka
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 0a7300e56eda6fba7c7564f00aa000f0
+    - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz
+      md5sum: 3de4a9f4da2f2b4909ef192452a8d211
+    - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi
+      md5sum: cfb07b0ba46e8468b4342edb243536f3
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
 - name: Run variant calling on somatic sample with strelka
   command: nextflow run main.nf -profile test_cache,tools_somatic --tools strelka --outdir results
   tags:
@@ -254,6 +340,30 @@
     # binary changes md5sums on reruns
     - path: results/strelka
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on somatic sample with strelka without intervals
   command: nextflow run main.nf -profile test_cache,tools_somatic --tools strelka --no_intervals --outdir results
   tags:
@@ -313,3 +423,23 @@
     # binary changes md5sums on reruns
     - path: results/strelka
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: d2775eb102acc5950f7f53883dcb503d
+    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz
+      md5sum: 54431f155c9538809e8caf99d1a75ec7
+    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi
+      md5sum: c67dcd711b096eb42f43784d5eadbc0d
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 0a7300e56eda6fba7c7564f00aa000f0
+    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz
+      md5sum: 3de4a9f4da2f2b4909ef192452a8d211
+    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi
+      md5sum: cfb07b0ba46e8468b4342edb243536f3
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
diff --git a/tests/test_strelka_bp.yml b/tests/test_strelka_bp.yml
index b89d09550d..b813f648d8 100644
--- a/tests/test_strelka_bp.yml
+++ b/tests/test_strelka_bp.yml
@@ -88,6 +88,30 @@
       should_exist: false
     - path: results/strelka
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on somatic sample with Strelka BP without intervals
   command: nextflow run main.nf -profile test_cache,tools_somatic --tools strelka,manta --no_intervals --outdir results
   tags:
@@ -185,3 +209,23 @@
       should_exist: false
     - path: results/strelka
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: d2775eb102acc5950f7f53883dcb503d
+    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz
+      md5sum: 54431f155c9538809e8caf99d1a75ec7
+    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi
+      md5sum: c67dcd711b096eb42f43784d5eadbc0d
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 0a7300e56eda6fba7c7564f00aa000f0
+    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz
+      md5sum: 3de4a9f4da2f2b4909ef192452a8d211
+    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi
+      md5sum: cfb07b0ba46e8468b4342edb243536f3
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
diff --git a/tests/test_tiddit.yml b/tests/test_tiddit.yml
index ad82fb4605..abac99f94b 100644
--- a/tests/test_tiddit.yml
+++ b/tests/test_tiddit.yml
@@ -44,6 +44,30 @@
     # conda changes md5sums for test
     - path: results/tiddit
       should_exist: false
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on germline sample with tiddit
   command: nextflow run main.nf -profile test_cache,tools_germline --tools tiddit --outdir results
   tags:
@@ -70,6 +94,17 @@
     # conda changes md5sums for test
     - path: results/tiddit
       should_exist: false
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
 - name: Run variant calling on tumor_only sample with tiddit
   command: nextflow run main.nf -profile test_cache,tools_tumoronly --tools tiddit --outdir results
   tags:
@@ -96,3 +131,14 @@
     # conda changes md5sums for test
     - path: results/tiddit
       should_exist: false
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml
index ae4c8f70be..8725ec6a64 100644
--- a/tests/test_tools_manually.yml
+++ b/tests/test_tools_manually.yml
@@ -34,6 +34,30 @@
       md5sum: 68b329da9893e34099c7d8ad5cb9c940
     - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_normalLogR.txt
       md5sum: 05418a7d814db11808172a4f57d040a1
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on somatic sample with mutect2 without intervals
   command: nextflow run main.nf -profile test_cache,tools_somatic --tools mutect2 --no_intervals --outdir results
   tags:
@@ -82,6 +106,26 @@
       md5sum: 17d2091015d04cbd4a26b7a67dc659e6
     - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.tbi
     # binary changes md5sums on reruns
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: d2775eb102acc5950f7f53883dcb503d
+    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz
+      md5sum: 54431f155c9538809e8caf99d1a75ec7
+    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi
+      md5sum: c67dcd711b096eb42f43784d5eadbc0d
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 0a7300e56eda6fba7c7564f00aa000f0
+    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz
+      md5sum: 3de4a9f4da2f2b4909ef192452a8d211
+    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi
+      md5sum: cfb07b0ba46e8468b4342edb243536f3
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run variant calling on somatic sample with mutect2
   command: nextflow run main.nf -profile test_cache,tools_somatic --tools mutect2 --outdir results
   tags:
@@ -123,6 +167,30 @@
       md5sum: c09dff3f145d77d4848992e244811c08
     - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.tbi
     # binary changes md5sums on reruns
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run joint calling on tumor only samples with mutect2
   command: nextflow run main.nf -profile test_cache,tools_tumoronly --input tests/csv/3.0/recalibrated_tumoronly_joint.csv --tools mutect2 --joint_mutect2 --outdir results
   tags:
@@ -170,6 +238,18 @@
       md5sum: 22e58aef3b14b335fa487d40b590ffeb
     - path: results/variant_calling/mutect2/test/test.mutect2.vcf.gz.tbi
     # binary changes md5sums on reruns
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run joint calling on somatic samples with mutect2
   command: nextflow run main.nf -profile test_cache,tools_somatic --input tests/csv/3.0/recalibrated_somatic_joint.csv --tools mutect2 --joint_mutect2 --outdir results
   tags:
@@ -218,6 +298,42 @@
       md5sum: 094cb75b0bda28e92b6718ff33d136e2
     - path: results/variant_calling/mutect2/test/test.mutect2.vcf.gz.tbi
     # binary changes md5sums on reruns
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt
+      md5sum: 69e29702ef01fd8f6c7a5468fc35a16a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt
+      md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a
+    - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt
+      md5sum: 103098d0bf76ed82d2b87d5f242b099a
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz
+      md5sum: b5888cf7395c57d39879a5faa6159eb3
+    - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi
+      md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee
+    - path: results/reports/samtools/sample1/sample1.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
+    # conda changes md5sums for test
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
+      md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
+      md5sum: 39005ffaac22871ffaaf19656fe69c5b
+    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
+      md5sum: 68d4b98f17361fddf73052ead34fa370
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
+      md5sum: 2819e995eafded35f53328c4ec19ba58
+    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
+      md5sum: 393c2749068304d8545b501b9d4658e4
+    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
+    # conda changes md5sums for test
 - name: Run full pipeline on tumoronly with most tools
   command: nextflow run . -profile test --input tests/csv/3.0/fastq_tumor_only.csv --tools cnvkit,freebayes,merge,mpileup,mutect2,snpeff,strelka,tiddit,vep --outdir results
   tags:
diff --git a/workflows/sarek.nf b/workflows/sarek.nf
index 5b0a9dcde9..a18d3864b3 100644
--- a/workflows/sarek.nf
+++ b/workflows/sarek.nf
@@ -801,17 +801,6 @@ workflow SAREK {
                 cram_variant_calling_no_spark,
                 cram_variant_calling_spark)
 
-            CRAM_QC_RECAL(
-                cram_variant_calling,
-                fasta,
-                intervals_for_preprocessing)
-
-            // Gather QC reports
-            reports = reports.mix(CRAM_QC_RECAL.out.reports.collect{ meta, report -> report })
-
-            // Gather used softwares versions
-            versions = versions.mix(CRAM_QC_RECAL.out.versions)
-
             // If params.save_output_as_bam, then convert CRAM files to BAM
             CRAM_TO_BAM_RECAL(cram_variant_calling, fasta, fasta_fai)
             versions = versions.mix(CRAM_TO_BAM_RECAL.out.versions)
@@ -852,11 +841,16 @@ workflow SAREK {
 
     }
 
-    if (params.tools) {
+    if (params.step == 'annotate') cram_variant_calling = Channel.empty()
 
-        if (params.step == 'annotate') cram_variant_calling = Channel.empty()
+    // RUN CRAM QC on the recalibrated CRAM files or when starting from step variant calling. NGSCheckmate should be run also on non-recalibrated CRAM files
+    CRAM_SAMPLEQC(cram_variant_calling,
+                    ngscheckmate_bed,
+                    fasta,
+                    params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator'),
+                    intervals_for_preprocessing)
 
-        CRAM_SAMPLEQC(cram_variant_calling, ngscheckmate_bed, fasta)
+    if (params.tools) {
 
         //
         // Logic to separate germline samples, tumor samples with no matched normal, and combine tumor-normal pairs