diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
index 6d388be62e..3de9f39915 100644
--- a/.github/actions/get-shards/action.yml
+++ b/.github/actions/get-shards/action.yml
@@ -7,6 +7,9 @@ inputs:
   paths:
     description: "Component paths to test"
     required: false
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: true
 outputs:
   shard:
     description: "Array of shard numbers"
@@ -27,9 +30,9 @@ runs:
       run: |
         # Run nf-test with dynamic parameter
         nftest_output=$(nf-test test \
-          --dry-run \
           --profile +docker \
-          --filter function,workflow,pipeline \
+          --tag ${{ inputs.tags }} \
+          --dry-run \
           --ci \
           --changed-since HEAD^) || {
             echo "nf-test command failed with exit code $?"
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
index 4bfca7c149..2b9fa1d59e 100644
--- a/.github/actions/nf-test/action.yml
+++ b/.github/actions/nf-test/action.yml
@@ -13,7 +13,9 @@ inputs:
   paths:
     description: "Test paths"
     required: true
-
+  tags:
+    description: "Tags to pass as argument for nf-test --tag parameter"
+    required: true
 runs:
   using: "composite"
   steps:
@@ -77,12 +79,12 @@ runs:
       run: |
         nf-test test \
           --profile=+${{ inputs.profile }} \
+          --tag ${{ inputs.tags }} \
           --tap=test.tap \
           --verbose \
           --ci \
           --changed-since HEAD^ \
           --shard ${{ inputs.shard }}/${{ inputs.total_shards }} \
-          --filter function,workflow,pipeline
 
           # Save the absolute path of the test.tap file to the output
           echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml
new file mode 100644
index 0000000000..ee90d28fab
--- /dev/null
+++ b/.github/workflows/nf-test-gpu.yml
@@ -0,0 +1,145 @@
+name: Run nf-test on GPU
+on:
+  push:
+    paths-ignore:
+      - "docs/**"
+      - "**/meta.yml"
+      - "**/*.md"
+      - "**/*.png"
+      - "**/*.svg"
+  pull_request:
+    branches: [dev]
+    paths-ignore:
+      - "docs/**"
+      - "**/meta.yml"
+      - "**/*.md"
+      - "**/*.png"
+      - "**/*.svg"
+  workflow_dispatch:
+    inputs:
+      runners:
+        description: "Runners to test on"
+        type: string
+        default: "gpu"
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
+  NFT_VER: "0.9.2"
+  NFT_WORKDIR: "~"
+  NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
+
+jobs:
+  nf-test-changes:
+    name: nf-test-changes
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+    outputs:
+      shard: ${{ steps.set-shards.outputs.shard }}
+      total_shards: ${{ steps.set-shards.outputs.total_shards }}
+    steps:
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: get number of shards
+        id: set-shards
+        uses: ./.github/actions/get-shards
+        env:
+          NFT_VER: ${{ env.NFT_VER }}
+        with:
+          max_shards: 2
+          tags: "gpu"
+
+      - name: debug
+        run: |
+          echo ${{ steps.set-shards.outputs.shard }}
+          echo ${{ steps.set-shards.outputs.total_shards }}
+
+  nf-test:
+    runs-on: "gpu"
+    name: "GPU | ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
+    needs: [nf-test-changes]
+    if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
+        profile: [conda, docker, singularity]
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
+        NXF_VER:
+          - "24.10.2"
+          - "latest-everything"
+    env:
+      NXF_ANSI_LOG: false
+      TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
+
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: Run nf-test
+        uses: ./.github/actions/nf-test
+        env:
+          NFT_DIFF: ${{ env.NFT_DIFF }}
+          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
+          NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+        with:
+          profile: ${{ matrix.profile }}
+          shard: ${{ matrix.shard }}
+          total_shards: ${{ env.TOTAL_SHARDS }}
+          tags: "gpu"
+
+  confirm-pass:
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+    needs: [nf-test]
+    if: always()
+    steps:
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "::group::DEBUG: `needs` Contents"
+          echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
+          echo "::endgroup::"
+
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        if: always()
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index 7f661b8ff8..e61a173a76 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -1,11 +1,9 @@
 name: Run nf-test
 on:
   push:
-    branches:
-      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
-      - "renovate/**" # branches Renovate creates
     paths-ignore:
       - "docs/**"
+      - "**/meta.yml"
       - "**/*.md"
       - "**/*.png"
       - "**/*.svg"
@@ -13,6 +11,7 @@ on:
     branches: [dev]
     paths-ignore:
       - "docs/**"
+      - "**/meta.yml"
       - "**/*.md"
       - "**/*.png"
       - "**/*.svg"
@@ -35,7 +34,6 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   NFT_DIFF: "pdiff"
   NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
-  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
   NFT_VER: "0.9.2"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
@@ -67,6 +65,7 @@ jobs:
           NFT_VER: ${{ env.NFT_VER }}
         with:
           max_shards: 7
+          tags: "cpu"
 
       - name: debug
         run: |
@@ -92,7 +91,6 @@ jobs:
           - isMaster: false
             profile: "singularity"
         NXF_VER:
-          # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
           - "24.10.2"
           - "latest-everything"
     env:
@@ -118,7 +116,7 @@ jobs:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
           total_shards: ${{ env.TOTAL_SHARDS }}
-
+          tags: "cpu"
   confirm-pass:
     runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     needs: [nf-test]
diff --git a/CHANGELOG.md b/CHANGELOG.md
index eaedf8cd67..58bb10f18c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -41,6 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1806](https://github.com/nf-core/sarek/pull/1806) - Use `nft-vcf` for nf-test vcf assertions
 - [1814](https://github.com/nf-core/sarek/pull/1814) - Added link to Bluesky
 - [1829](https://github.com/nf-core/sarek/pull/1829) - Add muse as variant caller to images
+- [1835](https://github.com/nf-core/sarek/pull/1835) - Add GPU testing possibilities
 
 #### Changed
 
diff --git a/tests/.nftignore b/tests/.nftignore
index 8b9fdd38c3..ba41f2a4a6 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -25,7 +25,7 @@ reports/EnsemblVEP/*/*.ann.summary.html
 reports/fastp/**/*.fastp.{log,html}
 reports/fastqc/**/*_fastqc.{html,zip}
 reports/markduplicates/**/*.md.cram.metrics
-reports/samtools/**/**.recal.cram.stats
+reports/samtools/**/**.cram.stats
 reports/snpeff/*/*_snpEff.csv
 reports/snpeff/*/snpEff_summary.html
 reports/vcftools/**/*.TsTv.qual
diff --git a/tests/aligner-bwa-mem.nf.test b/tests/aligner-bwa-mem.nf.test
index 45ef33e159..38e3a6f73d 100644
--- a/tests/aligner-bwa-mem.nf.test
+++ b/tests/aligner-bwa-mem.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --aligner bwa-mem --save_reference skip QC/recal/md") {
 
diff --git a/tests/aligner-bwa-mem2.nf.test b/tests/aligner-bwa-mem2.nf.test
index 9061d9f442..b37e359d63 100644
--- a/tests/aligner-bwa-mem2.nf.test
+++ b/tests/aligner-bwa-mem2.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --aligner bwa-mem2 --save_reference skip QC/recal/md") {
 
diff --git a/tests/aligner-dragmap.nf.test b/tests/aligner-dragmap.nf.test
index 5e4ece3793..7653998b8a 100644
--- a/tests/aligner-dragmap.nf.test
+++ b/tests/aligner-dragmap.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --aligner dragmap --save_reference skip QC/recal/md") {
 
diff --git a/tests/alignment_from_everything.nf.test b/tests/alignment_from_everything.nf.test
index 84ca65218c..c6811e2948 100644
--- a/tests/alignment_from_everything.nf.test
+++ b/tests/alignment_from_everything.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --input bam_and_fastq_and_spring.csv --save_mapped --save_output_as_bam") {
 
diff --git a/tests/alignment_from_everything.nf.test.snap b/tests/alignment_from_everything.nf.test.snap
index 9b1aac8e03..5c2db2fbdc 100644
--- a/tests/alignment_from_everything.nf.test.snap
+++ b/tests/alignment_from_everything.nf.test.snap
@@ -344,8 +344,6 @@
                 "fastqc_sequence_counts_plot.txt:md5,674147ee973b56cff1a8bed894d18d3f",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,5dbfcf6fcbbd054e17fb460985b078c2",
                 "fastqc_sequence_length_distribution_plot.txt:md5,893426c7b64f5fe3279733eb63c6abf9",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,c1b778ed3c2bd805c189e2b59f5eb2e0",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,83c8d998a9bb7575bbcdb67f1c117a9f",
                 "mosdepth-coverage-per-contig-single.txt:md5,7c01ea3a011867911ed0b612acb42007",
                 "mosdepth-cumcoverage-dist-id.txt:md5,c013414788f3acfff722a725b5c4938e",
                 "mosdepth_cov_dist.txt:md5,fc5e17338b2ed362a0e1f76add3a50fe",
@@ -398,15 +396,7 @@
                 "test_bam.recal.mosdepth.region.dist.txt:md5,75e1ce7e55af51f4985fa91654a5ea2d",
                 "test_bam.recal.mosdepth.summary.txt:md5,dbe376360e437c89190139ef0ae6769a",
                 "test_bam.recal.regions.bed.gz:md5,0e5ed846b9b11717e42e93eec60f4ffc",
-                "test_bam.recal.regions.bed.gz.csi:md5,633cc0252eb2246a0943aec7e7512e3e",
-                "test.md.cram.stats:md5,7d0a7d3d4ca6bf21702e7775b1777fb8",
-                "test.recal.cram.stats:md5,269fd4151ac69c1de63e2224310386a0",
-                "test2.md.cram.stats:md5,9036c85b25e11a3340a6c1006a8d614a",
-                "test2.recal.cram.stats:md5,816dbaf70f47a5f44444a97282a6bbb0",
-                "test3.md.cram.stats:md5,d8cfbfe40816feedcbc30aba0ae863a5",
-                "test3.recal.cram.stats:md5,46a3b9cf59fd06bf6c4b8f91b18d4f01",
-                "test_bam.md.cram.stats:md5,742cc3262b1c1b0710092b5288ed9d9a",
-                "test_bam.recal.cram.stats:md5,0459edb604f03ef29359826eb60a44a9"
+                "test_bam.recal.regions.bed.gz.csi:md5,633cc0252eb2246a0943aec7e7512e3e"
             ],
             "No CRAM files",
             [
@@ -466,4 +456,4 @@
         },
         "timestamp": "2025-03-10T11:13:03.085460403"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/alignment_to_fastq.nf.test b/tests/alignment_to_fastq.nf.test
index 72a533e8ad..02e8514484 100644
--- a/tests/alignment_to_fastq.nf.test
+++ b/tests/alignment_to_fastq.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --input bam_for_remapping.csv --save_mapped --save_output_as_bam") {
 
diff --git a/tests/alignment_to_fastq.nf.test.snap b/tests/alignment_to_fastq.nf.test.snap
index 1a405e1fe5..2e09d66f8d 100644
--- a/tests/alignment_to_fastq.nf.test.snap
+++ b/tests/alignment_to_fastq.nf.test.snap
@@ -243,8 +243,6 @@
                 "fastqc_sequence_counts_plot.txt:md5,bcd6fbad2fcbfcd6e78f7392945471cb",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,65c8986b4ea2983999508c5d8fce0df5",
                 "fastqc_sequence_length_distribution_plot.txt:md5,8f2a67d6bf43abce206aa77c2959b420",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,627a84e2b0dd5dc5a11aadbb20107c01",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,d727e4f305ac9d995de9596ee6824eaf",
                 "mosdepth-coverage-per-contig-single.txt:md5,76d816c3f71faf2009c8a6f88092a2f3",
                 "mosdepth-cumcoverage-dist-id.txt:md5,3af8f7d8ed7d1fdff6118e0098258192",
                 "mosdepth_cov_dist.txt:md5,4a2236db76d75e45012f6d7c180c90d6",
@@ -267,9 +265,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,75e1ce7e55af51f4985fa91654a5ea2d",
                 "test.recal.mosdepth.summary.txt:md5,dbe376360e437c89190139ef0ae6769a",
                 "test.recal.regions.bed.gz:md5,0e5ed846b9b11717e42e93eec60f4ffc",
-                "test.recal.regions.bed.gz.csi:md5,633cc0252eb2246a0943aec7e7512e3e",
-                "test.md.cram.stats:md5,2cc3430db9e2007da1464dd616aa8427",
-                "test.recal.cram.stats:md5,1ef19ce72bf2cb61d2dc4aede12bec94"
+                "test.recal.regions.bed.gz.csi:md5,633cc0252eb2246a0943aec7e7512e3e"
             ],
             "No CRAM files",
             [
diff --git a/tests/annotation_bcfann.nf.test b/tests/annotation_bcfann.nf.test
index d72a7da50b..457956b023 100644
--- a/tests/annotation_bcfann.nf.test
+++ b/tests/annotation_bcfann.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools bcfann") {
 
diff --git a/tests/annotation_merge.nf.test b/tests/annotation_merge.nf.test
index 7cc5c2cc33..c11569340a 100644
--- a/tests/annotation_merge.nf.test
+++ b/tests/annotation_merge.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools merge") {
 
diff --git a/tests/annotation_snpeff.nf.test b/tests/annotation_snpeff.nf.test
index f5bc64d93c..e99ad79607 100644
--- a/tests/annotation_snpeff.nf.test
+++ b/tests/annotation_snpeff.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools snpeff --download_cache") {
 
diff --git a/tests/annotation_vep.nf.test b/tests/annotation_vep.nf.test
index e6f1984d96..74defecd7e 100644
--- a/tests/annotation_vep.nf.test
+++ b/tests/annotation_vep.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools vep --download_cache --vep_include_fasta") {
 
diff --git a/tests/concatenation.nf.test b/tests/concatenation.nf.test
index 33232f029b..8455ee8b38 100644
--- a/tests/concatenation.nf.test
+++ b/tests/concatenation.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --concatenate_vcfs --tools freebayes,haplotypecaller") {
 
diff --git a/tests/concatenation.nf.test.snap b/tests/concatenation.nf.test.snap
index c78d8d1539..6a48b6b138 100644
--- a/tests/concatenation.nf.test.snap
+++ b/tests/concatenation.nf.test.snap
@@ -208,8 +208,6 @@
                 "testT.recal.mosdepth.summary.txt:md5,024649a659caff330dfbef4ac3560542",
                 "testT.recal.regions.bed.gz:md5,14b36a2cf428840aab471f95cfbe399f",
                 "testT.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
-                "testN.recal.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac",
-                "testT.recal.cram.stats:md5,fae549c0c944f6cc34dd6d9b9569e3d3",
                 "testN.freebayes.FILTER.summary:md5,2ec507a210cf7de0425b6c8028a6edf8",
                 "testN.freebayes.TsTv.count:md5,4913577b275634ea33077dd023325dee",
                 "testT.freebayes.FILTER.summary:md5,50f90bd0cdd1e95c10d7e5d88d0346f8",
diff --git a/tests/default.nf.test b/tests/default.nf.test
index 27534a15fd..dd4d7c6714 100644
--- a/tests/default.nf.test
+++ b/tests/default.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test") {
 
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index f1effac055..91240728c6 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -271,8 +271,6 @@
                 "fastqc_sequence_counts_plot.txt:md5,7f0f19a58e8e54e792a751fd04a9ae13",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,92b02e250ff78725deb9a10d510fcecc",
                 "fastqc_sequence_length_distribution_plot.txt:md5,fb04dce68ec566314125bc9438211b28",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,20b2630a7400c9c279bf8c0c66341f7d",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,b9b943621e50c7f3e75a37871667d5ed",
                 "mosdepth-coverage-per-contig-single.txt:md5,264db67a99d2c90ea7b075e33c201b77",
                 "mosdepth-cumcoverage-dist-id.txt:md5,5235e965da7ebe3bfebb24ffa88defff",
                 "mosdepth_cov_dist.txt:md5,8d0d7cb485a7bffb07da17b28f827120",
@@ -299,8 +297,6 @@
                 "test.recal.mosdepth.summary.txt:md5,839108358878ada89e1eaddf6e0541ba",
                 "test.recal.regions.bed.gz:md5,6fdaec99e739dc0f47fe55dd64dfe93e",
                 "test.recal.regions.bed.gz.csi:md5,5f9c60279af78e3aeafc96a8c11fb35f",
-                "test.md.cram.stats:md5,7d19da3fc342afe0884c944f97a578b1",
-                "test.recal.cram.stats:md5,820d123e746d1abdc90fd8710828082e",
                 "test.strelka.variants.FILTER.summary:md5,ad417bc96d31223f61170987975d8128",
                 "test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],
diff --git a/tests/fastp.nf.test b/tests/fastp.nf.test
index 9c86361f14..88732a9d6b 100644
--- a/tests/fastp.nf.test
+++ b/tests/fastp.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("trimming | -profile test,trimming --save_trimmed") {
 
diff --git a/tests/fastp.nf.test.snap b/tests/fastp.nf.test.snap
index d43bbc3182..3cf886ed42 100644
--- a/tests/fastp.nf.test.snap
+++ b/tests/fastp.nf.test.snap
@@ -330,8 +330,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,3e33ce923c2e9348c001cc34960d4d90",
                 "test.recal.mosdepth.summary.txt:md5,2de9c6803d74a7157c626320cf916587",
                 "test.recal.regions.bed.gz:md5,bb0ca9679342566559b7c5ed0b4e25b3",
-                "test.recal.regions.bed.gz.csi:md5,eba5aca0b8f72759192bbdd29330278e",
-                "test.md.cram.stats:md5,f44dadb50affac49500eefad04cb77ea"
+                "test.recal.regions.bed.gz.csi:md5,eba5aca0b8f72759192bbdd29330278e"
             ],
             "No BAM files",
             [
@@ -706,8 +705,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,1266123c1dd631e97aaf82a63162ed33",
                 "test.recal.mosdepth.summary.txt:md5,8d6d2a2d898fbf2e5bb4954c3a5857d9",
                 "test.recal.regions.bed.gz:md5,e8d15607e26a3d7c4f045fde542e129b",
-                "test.recal.regions.bed.gz.csi:md5,a3ac5a5d620082a4a1061656742d8e30",
-                "test.md.cram.stats:md5,f0c2d695d79101af0e4beb53239f5a9e"
+                "test.recal.regions.bed.gz.csi:md5,a3ac5a5d620082a4a1061656742d8e30"
             ],
             "No BAM files",
             [
diff --git a/tests/save_output_as_bam.nf.test b/tests/save_output_as_bam.nf.test
index 25c4701016..52a30e6e39 100644
--- a/tests/save_output_as_bam.nf.test
+++ b/tests/save_output_as_bam.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --save_output_as_bam skip QC/recal/md") {
 
diff --git a/tests/saved_mapped.nf.test b/tests/saved_mapped.nf.test
index b397b7c236..f68514a42e 100644
--- a/tests/saved_mapped.nf.test
+++ b/tests/saved_mapped.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --save_mapped skip QC/recal/md") {
 
diff --git a/tests/sentieon.nf.test b/tests/sentieon.nf.test
index 0ba4a4cd36..777bc7193f 100644
--- a/tests/sentieon.nf.test
+++ b/tests/sentieon.nf.test
@@ -5,6 +5,7 @@ nextflow_pipeline {
     tag "pipeline"
     tag "pipeline_sarek"
     tag "sentieon"
+    tag "cpu"
 
     test("stub") {
 
diff --git a/tests/sentieon.nf.test.snap b/tests/sentieon.nf.test.snap
index b8ec1d981c..90398b660a 100644
--- a/tests/sentieon.nf.test.snap
+++ b/tests/sentieon.nf.test.snap
@@ -217,8 +217,6 @@
                 "test.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
                 "test.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test.md.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "test.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test.strelka.variants.012:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test.strelka.variants.012.indv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "test.strelka.variants.012.pos:md5,d41d8cd98f00b204e9800998ecf8427e",
diff --git a/tests/start_from_markduplicates.nf.test b/tests/start_from_markduplicates.nf.test
index 0e1b4348b4..71b4a02d90 100644
--- a/tests/start_from_markduplicates.nf.test
+++ b/tests/start_from_markduplicates.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools null") {
 
diff --git a/tests/start_from_markduplicates.nf.test.snap b/tests/start_from_markduplicates.nf.test.snap
index 3db1f7cb43..c8413d7d41 100644
--- a/tests/start_from_markduplicates.nf.test.snap
+++ b/tests/start_from_markduplicates.nf.test.snap
@@ -96,8 +96,6 @@
                 "reports/samtools/test/test.sorted.cram.stats"
             ],
             [
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,d2650a5bec510d798e347f36a4d00e2d",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,f2123f7ee3d060c1547efc6247a04e42",
                 "mosdepth-coverage-per-contig-single.txt:md5,8b48f3336b063dcb1e086928b28a2cc6",
                 "mosdepth-cumcoverage-dist-id.txt:md5,3148977f0c4684ba681ee298d677fe38",
                 "mosdepth_cov_dist.txt:md5,9a531d5a5c05e568a1aeb2e738ac23c4",
@@ -111,8 +109,7 @@
                 "test.sorted.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2",
                 "test.sorted.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40",
                 "test.sorted.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e",
-                "test.sorted.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
-                "test.sorted.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac"
+                "test.sorted.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d"
             ],
             "No CRAM files",
             "No BAM files"
@@ -258,8 +255,6 @@
                 "reports/samtools/test/test.recal.cram.stats"
             ],
             [
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,902745b5a1915e5c1a25267b11bebbe7",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,832ed176357d6a5b4e50c718f5e4a704",
                 "mosdepth-coverage-per-contig-single.txt:md5,76d816c3f71faf2009c8a6f88092a2f3",
                 "mosdepth-cumcoverage-dist-id.txt:md5,3af8f7d8ed7d1fdff6118e0098258192",
                 "mosdepth_cov_dist.txt:md5,4a2236db76d75e45012f6d7c180c90d6",
@@ -281,9 +276,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,75e1ce7e55af51f4985fa91654a5ea2d",
                 "test.recal.mosdepth.summary.txt:md5,b23cf96942b2ada3f41172a9349a1175",
                 "test.recal.regions.bed.gz:md5,74cd0c779c7b3228adcf3b177333886a",
-                "test.recal.regions.bed.gz.csi:md5,080731cdedcd389e72135f048d6e2e00",
-                "test.md.cram.stats:md5,f181d98f08ad94c3926ac149a87d834b",
-                "test.recal.cram.stats:md5,18346c938c7b1bfaf9ac9413fdba90d8"
+                "test.recal.regions.bed.gz.csi:md5,080731cdedcd389e72135f048d6e2e00"
             ],
             [
                 [
@@ -414,8 +407,6 @@
                 "reports/samtools/test/test.sorted.cram.stats"
             ],
             [
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,d2650a5bec510d798e347f36a4d00e2d",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,f2123f7ee3d060c1547efc6247a04e42",
                 "mosdepth-coverage-per-contig-single.txt:md5,8b48f3336b063dcb1e086928b28a2cc6",
                 "mosdepth-cumcoverage-dist-id.txt:md5,3148977f0c4684ba681ee298d677fe38",
                 "mosdepth_cov_dist.txt:md5,9a531d5a5c05e568a1aeb2e738ac23c4",
@@ -434,9 +425,7 @@
                 "test.sorted.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2",
                 "test.sorted.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40",
                 "test.sorted.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e",
-                "test.sorted.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
-                "test.recal.cram.stats:md5,9f75ec16d22ce12c348cbd7477c9886e",
-                "test.sorted.cram.stats:md5,308a4213cc2ea25cbdd6d58b562673a5"
+                "test.sorted.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d"
             ],
             [
                 [
@@ -587,8 +576,6 @@
                 "reports/samtools/test/test.recal.cram.stats"
             ],
             [
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,902745b5a1915e5c1a25267b11bebbe7",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,832ed176357d6a5b4e50c718f5e4a704",
                 "mosdepth-coverage-per-contig-single.txt:md5,76d816c3f71faf2009c8a6f88092a2f3",
                 "mosdepth-cumcoverage-dist-id.txt:md5,3af8f7d8ed7d1fdff6118e0098258192",
                 "mosdepth_cov_dist.txt:md5,4a2236db76d75e45012f6d7c180c90d6",
@@ -610,9 +597,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,75e1ce7e55af51f4985fa91654a5ea2d",
                 "test.recal.mosdepth.summary.txt:md5,b23cf96942b2ada3f41172a9349a1175",
                 "test.recal.regions.bed.gz:md5,74cd0c779c7b3228adcf3b177333886a",
-                "test.recal.regions.bed.gz.csi:md5,080731cdedcd389e72135f048d6e2e00",
-                "test.md.cram.stats:md5,f181d98f08ad94c3926ac149a87d834b",
-                "test.recal.cram.stats:md5,18346c938c7b1bfaf9ac9413fdba90d8"
+                "test.recal.regions.bed.gz.csi:md5,080731cdedcd389e72135f048d6e2e00"
             ],
             [
                 [
diff --git a/tests/start_from_preparerecalibration.nf.test b/tests/start_from_preparerecalibration.nf.test
index cd7ed42635..03d0496f3e 100644
--- a/tests/start_from_preparerecalibration.nf.test
+++ b/tests/start_from_preparerecalibration.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --tools null") {
 
diff --git a/tests/start_from_preparerecalibration.nf.test.snap b/tests/start_from_preparerecalibration.nf.test.snap
index 317f526e42..099e08f087 100644
--- a/tests/start_from_preparerecalibration.nf.test.snap
+++ b/tests/start_from_preparerecalibration.nf.test.snap
@@ -50,8 +50,6 @@
                 "reference"
             ],
             [
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,d2650a5bec510d798e347f36a4d00e2d",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,f2123f7ee3d060c1547efc6247a04e42",
                 "multiqc_citations.txt:md5,3815a9f79e41890653a0e0d602c92ac9"
             ],
             "No BAM files",
@@ -387,15 +385,12 @@
                 "reports/samtools/test/test.recal.cram.stats"
             ],
             [
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,d2650a5bec510d798e347f36a4d00e2d",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,f2123f7ee3d060c1547efc6247a04e42",
                 "multiqc_citations.txt:md5,3815a9f79e41890653a0e0d602c92ac9",
                 "test.recal.mosdepth.global.dist.txt:md5,bdb8f185c35dd1eec7ce2f69bce57972",
                 "test.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2",
                 "test.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40",
                 "test.recal.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e",
-                "test.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
-                "test.recal.cram.stats:md5,9f75ec16d22ce12c348cbd7477c9886e"
+                "test.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d"
             ],
             "No BAM files",
             [
diff --git a/tests/start_from_recalibration.nf.test b/tests/start_from_recalibration.nf.test
index 01cd3510bb..bb15c8a818 100644
--- a/tests/start_from_recalibration.nf.test
+++ b/tests/start_from_recalibration.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --input tests/csv/3.0/mapped_single_cram.csv --step recalibrate --tools null") {
 
diff --git a/tests/start_from_recalibration.nf.test.snap b/tests/start_from_recalibration.nf.test.snap
index a14677664e..09b5e327a2 100644
--- a/tests/start_from_recalibration.nf.test.snap
+++ b/tests/start_from_recalibration.nf.test.snap
@@ -50,8 +50,7 @@
                 "test.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2",
                 "test.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40",
                 "test.recal.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e",
-                "test.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d",
-                "test.recal.cram.stats:md5,1aacf5ac46a0e600925934cf9ee92fc4"
+                "test.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d"
             ],
             "No BAM files",
             [
@@ -352,7 +351,7 @@
             ],
             "No BAM files",
             [
-                
+
             ]
         ],
         "meta": {
diff --git a/tests/tumor-normal-pair.nf.test b/tests/tumor-normal-pair.nf.test
index e5f9f51a24..79c9b5f56d 100644
--- a/tests/tumor-normal-pair.nf.test
+++ b/tests/tumor-normal-pair.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --input tests/csv/3.0/fastq_pair.csv") {
 
diff --git a/tests/tumor-normal-pair.nf.test.snap b/tests/tumor-normal-pair.nf.test.snap
index bac70d0020..377c1cee1d 100644
--- a/tests/tumor-normal-pair.nf.test.snap
+++ b/tests/tumor-normal-pair.nf.test.snap
@@ -313,8 +313,6 @@
                 "fastqc_sequence_counts_plot.txt:md5,fca7ee9ef3382e2837a302d8c5d33769",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,2aa0c6f33e4cffbb29cdabe2c28bb097",
                 "fastqc_sequence_length_distribution_plot.txt:md5,61b1fe978a2c73b86c30c27ee4bc60ae",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,611d52bfafbf4118e738fee9346ffb1c",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,9924357c076930220c7b3a9b02067f47",
                 "mosdepth-coverage-per-contig-single.txt:md5,e2bac78b61847b15c755dc7069670939",
                 "mosdepth-cumcoverage-dist-id.txt:md5,1a6c11f5d74f772870d49af0a7ff84d2",
                 "mosdepth_cov_dist.txt:md5,cb92686a4d6b7dcdeeee0ac13a63f369",
@@ -353,10 +351,6 @@
                 "test2.recal.mosdepth.summary.txt:md5,8b991358768cade225470a07cd34f573",
                 "test2.recal.regions.bed.gz:md5,08e767f91a0a8d82733f0040e804a85f",
                 "test2.recal.regions.bed.gz.csi:md5,eba5aca0b8f72759192bbdd29330278e",
-                "test.md.cram.stats:md5,7d0a7d3d4ca6bf21702e7775b1777fb8",
-                "test.recal.cram.stats:md5,269fd4151ac69c1de63e2224310386a0",
-                "test2.md.cram.stats:md5,592aae2575ef68c8c8d9e993ca288f2d",
-                "test2.recal.cram.stats:md5,47c5ad8a7d4221d03673fd67388f9960",
                 "test.strelka.variants.FILTER.summary:md5,dd87f507da7de20d5318841af312493b",
                 "test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
                 "test2_vs_test.strelka.somatic_indels.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
diff --git a/tests/variant_calling_cnvkit.nf.test b/tests/variant_calling_cnvkit.nf.test
index e46fa06fe6..91e2c58022 100644
--- a/tests/variant_calling_cnvkit.nf.test
+++ b/tests/variant_calling_cnvkit.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools cnvkit --input recalibrated_germline.csv") {
 
diff --git a/tests/variant_calling_cnvkit.nf.test.snap b/tests/variant_calling_cnvkit.nf.test.snap
index 4145840d7c..1a51e70f33 100644
--- a/tests/variant_calling_cnvkit.nf.test.snap
+++ b/tests/variant_calling_cnvkit.nf.test.snap
@@ -139,10 +139,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "multi_intervals.antitarget.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "multi_intervals.target.bed:md5,f7474a0afbf5565c5675916606f2d9bd",
                 "reference.cnn:md5,891454915f82d0eeda0be13d71e0d5d7",
@@ -272,7 +268,6 @@
                 "sample1.recal.mosdepth.summary.txt:md5,d7676e7c1de851b0ee5185d21096123b",
                 "sample1.recal.regions.bed.gz:md5,6edeb8f7041a4403cb73651744b5bc82",
                 "sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
                 "multi_intervals.antitarget.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "multi_intervals.target.bed:md5,f7474a0afbf5565c5675916606f2d9bd",
                 "reference.cnn:md5,891454915f82d0eeda0be13d71e0d5d7",
@@ -399,8 +394,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "multi_intervals.antitarget.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "multi_intervals.target.bed:md5,f7474a0afbf5565c5675916606f2d9bd",
                 "reference.cnn:md5,891454915f82d0eeda0be13d71e0d5d7",
@@ -514,7 +507,6 @@
                 "sample2.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample2.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample2.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "cnvkit.reference.antitarget-tmp.bed:md5,3d4d20f9f23b39970865d29ef239d20b",
                 "cnvkit.reference.target-tmp.bed:md5,657b25dbda8516624efa8cb2cf3716ca",
                 "test2.paired_end.recalibrated.sorted-scatter.png:md5,d9a4a27a7a93eca23108b43dea09c140",
diff --git a/tests/variant_calling_controlfreec.nf.test b/tests/variant_calling_controlfreec.nf.test
index 53524e19e1..d7a7712330 100644
--- a/tests/variant_calling_controlfreec.nf.test
+++ b/tests/variant_calling_controlfreec.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools controlfreec somatic") {
 
diff --git a/tests/variant_calling_controlfreec.nf.test.snap b/tests/variant_calling_controlfreec.nf.test.snap
index bda436c60d..b8d438ec86 100644
--- a/tests/variant_calling_controlfreec.nf.test.snap
+++ b/tests/variant_calling_controlfreec.nf.test.snap
@@ -113,8 +113,6 @@
                 "sample4.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample4.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
                 "sample4.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "sample3.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "sample4.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "GC_profile.sample4_vs_sample3.cpn:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample4_vs_sample3.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample4_vs_sample3.circos.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -232,8 +230,6 @@
                 "sample4.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
                 "sample4.recal.regions.bed.gz:md5,b7561bc56a955f7db0f11e67e2ec0386",
                 "sample4.recal.regions.bed.gz.csi:md5,538cb5d244411a670a4b041691f8825b",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample4_vs_sample3.bed:md5,47f60179409e9389e59b2e2525e42210",
                 "sample4_vs_sample3.circos.txt:md5,68addb1d8bda08355842bef0ab15cd6e",
                 "sample4_vs_sample3.normal.mpileup.gz_control.cpn:md5,d50bf2c9a4d35f022364901c284e80ed",
@@ -339,7 +335,6 @@
                 "sample2.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample2.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
                 "sample2.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "sample2.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "GC_profile.sample2.cpn:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample2.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample2.circos.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -436,7 +431,6 @@
                 "sample2.recal.mosdepth.summary.txt:md5,0a7300e56eda6fba7c7564f00aa000f0",
                 "sample2.recal.per-base.bed.gz:md5,39a1bc436aa8546c26faedbe94cb676c",
                 "sample2.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.bed:md5,5249f46e614b60867bdd6b9b83327979",
                 "sample2.circos.txt:md5,2efab24d023931cec8b158c56d1f1765",
                 "sample2.p.value.txt:md5,38c8c9ad33a4fca3804a34d5c436cd1e",
diff --git a/tests/variant_calling_freebayes.nf.test b/tests/variant_calling_freebayes.nf.test
index ccab744229..8b56420dcc 100644
--- a/tests/variant_calling_freebayes.nf.test
+++ b/tests/variant_calling_freebayes.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools freebayes --wes --nucleotides_per_second 20") {
 
diff --git a/tests/variant_calling_freebayes.nf.test.snap b/tests/variant_calling_freebayes.nf.test.snap
index ed148ae6a0..95493b1bed 100644
--- a/tests/variant_calling_freebayes.nf.test.snap
+++ b/tests/variant_calling_freebayes.nf.test.snap
@@ -133,7 +133,6 @@
                 "sample2.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
                 "sample2.recal.regions.bed.gz:md5,b7561bc56a955f7db0f11e67e2ec0386",
                 "sample2.recal.regions.bed.gz.csi:md5,538cb5d244411a670a4b041691f8825b",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.freebayes.FILTER.summary:md5,0df3ddeec5779344b5d463347c9c6ea8",
                 "sample2.freebayes.TsTv.count:md5,b1d308ed5087361a584cb61e7b835e1e"
             ]
@@ -443,8 +442,6 @@
                 "fastqc_sequence_counts_plot.txt:md5,7f0f19a58e8e54e792a751fd04a9ae13",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,92b02e250ff78725deb9a10d510fcecc",
                 "fastqc_sequence_length_distribution_plot.txt:md5,fb04dce68ec566314125bc9438211b28",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,c83824137317120a2e13d7c65a8f2440",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,3577bc216cbd8074250e163ae2515358",
                 "mosdepth-coverage-per-contig-single.txt:md5,3914c1896454cc5b176a66737524690d",
                 "mosdepth-cumcoverage-dist-id.txt:md5,d20db85d15395e60fe7c667292fb8cd2",
                 "mosdepth_cov_dist.txt:md5,66f531e1c6f8efabddb86421022e8753",
@@ -475,8 +472,6 @@
                 "test.recal.per-base.bed.gz.csi:md5,bb424ead65ffe782f6eaa3663ea65721",
                 "test.recal.regions.bed.gz:md5,e39c27885a30c0321f3cb7c7fb6c5edc",
                 "test.recal.regions.bed.gz.csi:md5,e1a52ced0e9ded1eecbca4eff2014c8e",
-                "test.md.cram.stats:md5,7d19da3fc342afe0884c944f97a578b1",
-                "test.recal.cram.stats:md5,87ed0ca7a04c0b6dfc5f05b18467ecbe",
                 "test.freebayes.FILTER.summary:md5,75824ce08910acce7e9f6adb4d635850",
                 "test.freebayes.TsTv.count:md5,3c198f7ec7fe2f5d365218ba0ff64197"
             ],
@@ -829,8 +824,6 @@
                 "fastqc_sequence_counts_plot.txt:md5,fca7ee9ef3382e2837a302d8c5d33769",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,2aa0c6f33e4cffbb29cdabe2c28bb097",
                 "fastqc_sequence_length_distribution_plot.txt:md5,61b1fe978a2c73b86c30c27ee4bc60ae",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,f41c2bf1b01ccaefb35545356d5778ce",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,e5fa551f9eb1d04801a92cdb8b078910",
                 "mosdepth-coverage-per-contig-single.txt:md5,de1ecd6fa3832eb41174e63c2e645511",
                 "mosdepth-cumcoverage-dist-id.txt:md5,21ba80158290da7b73295b0159d183c6",
                 "mosdepth_cov_dist.txt:md5,39228a3796068f04cb37f864cee22727",
@@ -876,10 +869,6 @@
                 "test2.recal.per-base.bed.gz.csi:md5,49dec4905343693cb7812da9ee60037c",
                 "test2.recal.regions.bed.gz:md5,0bb2549180165a99680ba3e453ea312f",
                 "test2.recal.regions.bed.gz.csi:md5,e1a52ced0e9ded1eecbca4eff2014c8e",
-                "test.md.cram.stats:md5,7d0a7d3d4ca6bf21702e7775b1777fb8",
-                "test.recal.cram.stats:md5,4efd4142116c0ddc309aa3660834d991",
-                "test2.md.cram.stats:md5,592aae2575ef68c8c8d9e993ca288f2d",
-                "test2.recal.cram.stats:md5,9ac6a5c9280fa139e8597a41aadabbb5",
                 "test.freebayes.FILTER.summary:md5,43d53e36cbb1091f915b2499e545b41e",
                 "test.freebayes.TsTv.count:md5,650f3dc78c5aaaecfe8ffa3d499e812f",
                 "test2_vs_test.freebayes.FILTER.summary:md5,84039d55edf0981d6b9b81252aff6741",
@@ -1223,8 +1212,6 @@
                 "fastqc_sequence_counts_plot.txt:md5,fca7ee9ef3382e2837a302d8c5d33769",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,2aa0c6f33e4cffbb29cdabe2c28bb097",
                 "fastqc_sequence_length_distribution_plot.txt:md5,61b1fe978a2c73b86c30c27ee4bc60ae",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,611d52bfafbf4118e738fee9346ffb1c",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,9924357c076930220c7b3a9b02067f47",
                 "mosdepth-coverage-per-contig-single.txt:md5,2df7b17a479e4119989eef6e38b894cc",
                 "mosdepth-cumcoverage-dist-id.txt:md5,4acfb4efd527377aa16171fa8360bf10",
                 "mosdepth_cov_dist.txt:md5,717239843b7c0f2fd13da48f9480dfbb",
@@ -1258,10 +1245,6 @@
                 "test2.recal.mosdepth.summary.txt:md5,d5e4084de2ea2a0a7b60b2d71c804d4b",
                 "test2.recal.per-base.bed.gz:md5,e1c6d60621d8f64aaf28fa1c1ddda921",
                 "test2.recal.per-base.bed.gz.csi:md5,69f4da029c05e9bcccae8895b6247a1e",
-                "test.md.cram.stats:md5,7d0a7d3d4ca6bf21702e7775b1777fb8",
-                "test.recal.cram.stats:md5,478a0a01a1d1e2f2a5c0d91c58d32d84",
-                "test2.md.cram.stats:md5,592aae2575ef68c8c8d9e993ca288f2d",
-                "test2.recal.cram.stats:md5,bada0a59a5497724fc71620d999e1460",
                 "test.freebayes.FILTER.summary:md5,76c5919541536c12b5c8a6094d6d78d5",
                 "test.freebayes.TsTv.count:md5,0a0464beef110bc0f3c5a35d022b528e",
                 "test2_vs_test.freebayes.FILTER.summary:md5,d2d717fef7c18ef9b40bbbc5c5bbf101",
@@ -1576,8 +1559,6 @@
                 "fastqc_sequence_counts_plot.txt:md5,7f0f19a58e8e54e792a751fd04a9ae13",
                 "fastqc_sequence_duplication_levels_plot.txt:md5,92b02e250ff78725deb9a10d510fcecc",
                 "fastqc_sequence_length_distribution_plot.txt:md5,fb04dce68ec566314125bc9438211b28",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,20b2630a7400c9c279bf8c0c66341f7d",
-                "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,b9b943621e50c7f3e75a37871667d5ed",
                 "mosdepth-coverage-per-contig-single.txt:md5,264db67a99d2c90ea7b075e33c201b77",
                 "mosdepth-cumcoverage-dist-id.txt:md5,5235e965da7ebe3bfebb24ffa88defff",
                 "mosdepth_cov_dist.txt:md5,8d0d7cb485a7bffb07da17b28f827120",
@@ -1604,8 +1585,6 @@
                 "test.recal.mosdepth.summary.txt:md5,839108358878ada89e1eaddf6e0541ba",
                 "test.recal.regions.bed.gz:md5,6fdaec99e739dc0f47fe55dd64dfe93e",
                 "test.recal.regions.bed.gz.csi:md5,5f9c60279af78e3aeafc96a8c11fb35f",
-                "test.md.cram.stats:md5,7d19da3fc342afe0884c944f97a578b1",
-                "test.recal.cram.stats:md5,4242101f58b473ca012a8162e45ff7d4",
                 "test.freebayes.FILTER.summary:md5,562eaa4512cd4b57e6cfca7b44957d1c",
                 "test.freebayes.TsTv.count:md5,4e6935b1e1906e57be1b54c0dffe7169"
             ],
@@ -1753,7 +1732,6 @@
                 "sample2.recal.mosdepth.summary.txt:md5,0a7300e56eda6fba7c7564f00aa000f0",
                 "sample2.recal.per-base.bed.gz:md5,39a1bc436aa8546c26faedbe94cb676c",
                 "sample2.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.freebayes.FILTER.summary:md5,ee513ecf779b6e201b8ef98f95f25aab",
                 "sample2.freebayes.TsTv.count:md5,2dc153ad5af26c9f8aa82442bf65b4bf"
             ]
diff --git a/tests/variant_calling_haplotypecaller.nf.test b/tests/variant_calling_haplotypecaller.nf.test
index e4082a7687..33ccf8835c 100644
--- a/tests/variant_calling_haplotypecaller.nf.test
+++ b/tests/variant_calling_haplotypecaller.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --input mapped_single_bam.csv --tools haplotypecaller --step variant_calling --wes --nucleotides_per_second 20") {
 
diff --git a/tests/variant_calling_haplotypecaller.nf.test.snap b/tests/variant_calling_haplotypecaller.nf.test.snap
index 3c220f2b8d..f8d65f48a7 100644
--- a/tests/variant_calling_haplotypecaller.nf.test.snap
+++ b/tests/variant_calling_haplotypecaller.nf.test.snap
@@ -123,7 +123,6 @@
                 "test.recal.mosdepth.summary.txt:md5,4f0d231060cbde4efdd673863bd2fb59",
                 "test.recal.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa",
                 "test.recal.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294",
-                "test.recal.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac",
                 "test.haplotypecaller.FILTER.summary:md5,87a84b5f8ac3d3cbeeef7d60afcdbfe7",
                 "test.haplotypecaller.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663"
             ],
@@ -270,7 +269,6 @@
                 "test.recal.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294",
                 "test.recal.regions.bed.gz:md5,0c8215fbea7b0bf7aba9d1781575f905",
                 "test.recal.regions.bed.gz.csi:md5,e1a52ced0e9ded1eecbca4eff2014c8e",
-                "test.recal.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac",
                 "test.haplotypecaller.FILTER.summary:md5,87a84b5f8ac3d3cbeeef7d60afcdbfe7",
                 "test.haplotypecaller.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663"
             ],
@@ -419,7 +417,6 @@
                 "test.recal.mosdepth.summary.txt:md5,4f0d231060cbde4efdd673863bd2fb59",
                 "test.recal.per-base.bed.gz:md5,da6db0fb375a3053a89db8c935eebbaa",
                 "test.recal.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294",
-                "test.recal.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac",
                 "test.haplotypecaller.filtered.FILTER.summary:md5,4e2ceea7f3ff998004691fd71192d9ee",
                 "test.haplotypecaller.filtered.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663"
             ],
@@ -578,7 +575,6 @@
                 "test.recal.per-base.bed.gz.csi:md5,6f322dc9250522a701bd68bd18fa8294",
                 "test.recal.regions.bed.gz:md5,0c8215fbea7b0bf7aba9d1781575f905",
                 "test.recal.regions.bed.gz.csi:md5,e1a52ced0e9ded1eecbca4eff2014c8e",
-                "test.recal.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac",
                 "test.haplotypecaller.filtered.FILTER.summary:md5,4e2ceea7f3ff998004691fd71192d9ee",
                 "test.haplotypecaller.filtered.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663"
             ],
diff --git a/tests/variant_calling_lofreq.nf.test b/tests/variant_calling_lofreq.nf.test
index e04ede44b2..899f11d3d8 100644
--- a/tests/variant_calling_lofreq.nf.test
+++ b/tests/variant_calling_lofreq.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools lofreq tumoronly") {
 
diff --git a/tests/variant_calling_lofreq.nf.test.snap b/tests/variant_calling_lofreq.nf.test.snap
index c7aa74a1d6..f3efd3089b 100644
--- a/tests/variant_calling_lofreq.nf.test.snap
+++ b/tests/variant_calling_lofreq.nf.test.snap
@@ -118,7 +118,6 @@
                 "sample2.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
                 "sample2.recal.regions.bed.gz:md5,b7561bc56a955f7db0f11e67e2ec0386",
                 "sample2.recal.regions.bed.gz.csi:md5,538cb5d244411a670a4b041691f8825b",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.lofreq.FILTER.summary:md5,8dd8a0c91d5c4a260b462e04f615e502"
             ],
             [
@@ -250,7 +249,6 @@
                 "sample2.recal.mosdepth.summary.txt:md5,0a7300e56eda6fba7c7564f00aa000f0",
                 "sample2.recal.per-base.bed.gz:md5,39a1bc436aa8546c26faedbe94cb676c",
                 "sample2.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.lofreq.FILTER.summary:md5,72beda1b57da053eb352204828605a40"
             ],
             [
diff --git a/tests/variant_calling_manta.nf.test b/tests/variant_calling_manta.nf.test
index 36e6b7f393..7a686a3b04 100644
--- a/tests/variant_calling_manta.nf.test
+++ b/tests/variant_calling_manta.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools manta --only_paired_variant_calling") {
 
diff --git a/tests/variant_calling_manta.nf.test.snap b/tests/variant_calling_manta.nf.test.snap
index a539ba6ccc..cba513e6c7 100644
--- a/tests/variant_calling_manta.nf.test.snap
+++ b/tests/variant_calling_manta.nf.test.snap
@@ -89,7 +89,6 @@
                 "sample1.recal.mosdepth.summary.txt:md5,d7676e7c1de851b0ee5185d21096123b",
                 "sample1.recal.regions.bed.gz:md5,6edeb8f7041a4403cb73651744b5bc82",
                 "sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
                 "sample1.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample1.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],
@@ -199,7 +198,6 @@
                 "sample2.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample2.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample2.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.manta.tumor_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample2.manta.tumor_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],
@@ -342,8 +340,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample3.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
                 "sample4_vs_sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
@@ -462,7 +458,6 @@
                 "sample2.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample2.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample2.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.manta.tumor_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample2.manta.tumor_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],
@@ -641,10 +636,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample1.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample1.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
                 "sample2.manta.tumor_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
@@ -822,8 +813,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample3.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
                 "sample4_vs_sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
@@ -945,7 +934,6 @@
                 "sample1.recal.mosdepth.summary.txt:md5,d7676e7c1de851b0ee5185d21096123b",
                 "sample1.recal.regions.bed.gz:md5,6edeb8f7041a4403cb73651744b5bc82",
                 "sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
                 "sample1.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample1.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],
diff --git a/tests/variant_calling_mpileup.nf.test b/tests/variant_calling_mpileup.nf.test
index 0403297185..8b6da80831 100644
--- a/tests/variant_calling_mpileup.nf.test
+++ b/tests/variant_calling_mpileup.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools mpileup --input recalibrated_germline.csv") {
 
diff --git a/tests/variant_calling_mpileup.nf.test.snap b/tests/variant_calling_mpileup.nf.test.snap
index fce439a1e4..057ec2553a 100644
--- a/tests/variant_calling_mpileup.nf.test.snap
+++ b/tests/variant_calling_mpileup.nf.test.snap
@@ -122,7 +122,6 @@
                 "sample2.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample2.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample2.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.bcftools.FILTER.summary:md5,8766995f3e4119ef30dfdaa9fb3752ce",
                 "sample2.bcftools.TsTv.count:md5,01df95fcb4df593f7e1b214d90ebdb59"
             ],
@@ -265,7 +264,6 @@
                 "sample1.recal.mosdepth.summary.txt:md5,d7676e7c1de851b0ee5185d21096123b",
                 "sample1.recal.regions.bed.gz:md5,6edeb8f7041a4403cb73651744b5bc82",
                 "sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
                 "sample1.bcftools.FILTER.summary:md5,83a10512eb9d035f409a84db7e620c28",
                 "sample1.bcftools.TsTv.count:md5,bfa998e75cbcb3da66f823cf39ef1e48"
             ],
@@ -408,7 +406,6 @@
                 "sample2.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample2.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample2.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.bcftools.FILTER.summary:md5,f295c70f174e7705fc2bac607aedbfda",
                 "sample2.bcftools.TsTv.count:md5,e5d20f81fc97f7ee97fb6cb6bd851047"
             ],
@@ -548,7 +545,6 @@
                 "sample1.recal.mosdepth.summary.txt:md5,d7676e7c1de851b0ee5185d21096123b",
                 "sample1.recal.regions.bed.gz:md5,6edeb8f7041a4403cb73651744b5bc82",
                 "sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
                 "sample1.bcftools.FILTER.summary:md5,9b62595b026decf12e9198d531e4307a",
                 "sample1.bcftools.TsTv.count:md5,6c937125d7bac4c491bea50f18cba43a"
             ],
diff --git a/tests/variant_calling_muse.nf.test b/tests/variant_calling_muse.nf.test
index c007b6e74a..fdcf3dc41f 100644
--- a/tests/variant_calling_muse.nf.test
+++ b/tests/variant_calling_muse.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("Run with profile test | --tools muse | somatic") {
 
diff --git a/tests/variant_calling_muse.nf.test.snap b/tests/variant_calling_muse.nf.test.snap
index 95caaf3b5f..3dfde97e84 100644
--- a/tests/variant_calling_muse.nf.test.snap
+++ b/tests/variant_calling_muse.nf.test.snap
@@ -130,8 +130,6 @@
                 "sample4.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
                 "sample4.recal.regions.bed.gz:md5,b7561bc56a955f7db0f11e67e2ec0386",
                 "sample4.recal.regions.bed.gz.csi:md5,538cb5d244411a670a4b041691f8825b",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample4_vs_sample3.muse.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample4_vs_sample3.muse.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f",
                 "sample4_vs_sample3.MuSE.txt:md5,06f2eb941e03ea238ca8d864985aa6f1"
@@ -334,8 +332,6 @@
                 "sample4.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample4.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
                 "sample4.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "sample3.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
-                "sample4.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample4_vs_sample3.muse.012:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample4_vs_sample3.muse.012.indv:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "sample4_vs_sample3.muse.012.pos:md5,d41d8cd98f00b204e9800998ecf8427e",
diff --git a/tests/variant_calling_strelka.nf.test b/tests/variant_calling_strelka.nf.test
index 39f9a4cb6e..702d91c8c7 100644
--- a/tests/variant_calling_strelka.nf.test
+++ b/tests/variant_calling_strelka.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools strelka --only_paired_variant_calling") {
 
diff --git a/tests/variant_calling_strelka.nf.test.snap b/tests/variant_calling_strelka.nf.test.snap
index 3294adad59..ae72997a6a 100644
--- a/tests/variant_calling_strelka.nf.test.snap
+++ b/tests/variant_calling_strelka.nf.test.snap
@@ -183,10 +183,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample1.strelka.variants.FILTER.summary:md5,fef8aeadd3b0f3b8c040c0da03bf1cbd",
                 "sample1.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49",
                 "sample4_vs_sample3.strelka.somatic_indels.FILTER.summary:md5,30a45e2bc87f40c89388032cbf75ec65",
@@ -380,8 +376,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample3.strelka.variants.FILTER.summary:md5,8697a0a983314e98b99b5f6038af65f6",
                 "sample3.strelka.variants.TsTv.count:md5,1481854d2a765f5641856ecf95ca4097",
                 "sample4_vs_sample3.strelka.somatic_indels.FILTER.summary:md5,30a45e2bc87f40c89388032cbf75ec65",
@@ -572,8 +566,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample3.strelka.variants.FILTER.summary:md5,fef8aeadd3b0f3b8c040c0da03bf1cbd",
                 "sample3.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49",
                 "sample4_vs_sample3.strelka.somatic_indels.FILTER.summary:md5,30a45e2bc87f40c89388032cbf75ec65",
@@ -726,7 +718,6 @@
                 "sample1.recal.mosdepth.summary.txt:md5,d7676e7c1de851b0ee5185d21096123b",
                 "sample1.recal.regions.bed.gz:md5,6edeb8f7041a4403cb73651744b5bc82",
                 "sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
                 "sample1.strelka.variants.FILTER.summary:md5,fef8aeadd3b0f3b8c040c0da03bf1cbd",
                 "sample1.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49"
             ],
@@ -870,7 +861,6 @@
                 "sample1.recal.mosdepth.summary.txt:md5,d7676e7c1de851b0ee5185d21096123b",
                 "sample1.recal.regions.bed.gz:md5,6edeb8f7041a4403cb73651744b5bc82",
                 "sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
                 "sample1.strelka.variants.FILTER.summary:md5,8697a0a983314e98b99b5f6038af65f6",
                 "sample1.strelka.variants.TsTv.count:md5,1481854d2a765f5641856ecf95ca4097"
             ],
diff --git a/tests/variant_calling_strelka_bp.nf.test b/tests/variant_calling_strelka_bp.nf.test
index 9be396ee43..b1a09f7b09 100644
--- a/tests/variant_calling_strelka_bp.nf.test
+++ b/tests/variant_calling_strelka_bp.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools manta,strelka somatic") {
 
diff --git a/tests/variant_calling_strelka_bp.nf.test.snap b/tests/variant_calling_strelka_bp.nf.test.snap
index 6cf5804e8f..ac35f58d15 100644
--- a/tests/variant_calling_strelka_bp.nf.test.snap
+++ b/tests/variant_calling_strelka_bp.nf.test.snap
@@ -196,8 +196,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample3.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
                 "sample4_vs_sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
@@ -442,8 +440,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample3.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
                 "sample4_vs_sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
diff --git a/tests/variant_calling_tiddit.nf.test b/tests/variant_calling_tiddit.nf.test
index caf9a06c37..e111c955c4 100644
--- a/tests/variant_calling_tiddit.nf.test
+++ b/tests/variant_calling_tiddit.nf.test
@@ -4,6 +4,7 @@ nextflow_pipeline {
     script "../main.nf"
     tag "pipeline"
     tag "pipeline_sarek"
+    tag "cpu"
 
     test("-profile test --tools tiddit germline") {
 
diff --git a/tests/variant_calling_tiddit.nf.test.snap b/tests/variant_calling_tiddit.nf.test.snap
index 8f32dfa7ea..c6ec2d0c5d 100644
--- a/tests/variant_calling_tiddit.nf.test.snap
+++ b/tests/variant_calling_tiddit.nf.test.snap
@@ -93,7 +93,6 @@
                 "sample1.recal.mosdepth.summary.txt:md5,d7676e7c1de851b0ee5185d21096123b",
                 "sample1.recal.regions.bed.gz:md5,6edeb8f7041a4403cb73651744b5bc82",
                 "sample1.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a",
-                "sample1.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
                 "sample1.tiddit.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample1.tiddit.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],
@@ -204,7 +203,6 @@
                 "sample2.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample2.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample2.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample2.tiddit.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample2.tiddit.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],
@@ -346,8 +344,6 @@
                 "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80",
                 "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52",
                 "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e",
-                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
-                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
                 "sample3.tiddit.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",
                 "sample3.tiddit.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a",
                 "sample4_vs_sample3.tiddit_sv_merge.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423",