diff --git a/CHANGELOG.md b/CHANGELOG.md
index 97c6e3b5..8f6a4fd7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - [#532](https://github.com/genomic-medicine-sweden/nallo/pull/532) - Updated template to nf-core/tools version 3.1.1
+- [#535](https://github.com/genomic-medicine-sweden/nallo/pull/535) - Updated DeepVariant to 1.8.0 for SPRQ compatability
 
 ### `Removed`
 
@@ -31,9 +32,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Module updates
 
-| Tool    | Old version | New version |
-| ------- | ----------- | ----------- |
-| hifiasm | 0.19.8      | 0.24.0      |
+| Tool        | Old version | New version |
+| ----------- | ----------- | ----------- |
+| hifiasm     | 0.19.8      | 0.24.0      |
+| deepvariant | 1.6.1       | 1.8.0       |
 
 > [!NOTE]
 > Version has been updated if both old and new version information is present.
diff --git a/modules.json b/modules.json
index b3f00265..345dae7f 100644
--- a/modules.json
+++ b/modules.json
@@ -79,12 +79,12 @@
                     },
                     "deepvariant/rundeepvariant": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "e9b59c82daa0fac067284fc52f93011b43952a8f",
                         "installed_by": ["modules"]
                     },
                     "deepvariant/vcfstatsreport": {
                         "branch": "master",
-                        "git_sha": "2f9a5431355897e299cb41928c45f51ea8410c42",
+                        "git_sha": "e9b59c82daa0fac067284fc52f93011b43952a8f",
                         "installed_by": ["modules"]
                     },
                     "ensemblvep/filtervep": {
diff --git a/modules/nf-core/deepvariant/rundeepvariant/main.nf b/modules/nf-core/deepvariant/rundeepvariant/main.nf
index 7f99c53f..aec18907 100644
--- a/modules/nf-core/deepvariant/rundeepvariant/main.nf
+++ b/modules/nf-core/deepvariant/rundeepvariant/main.nf
@@ -5,7 +5,7 @@ process DEEPVARIANT_RUNDEEPVARIANT {
     // FIXME Conda is not supported at the moment
     // BUG https://github.com/nf-core/modules/issues/1754
     // BUG https://github.com/bioconda/bioconda-recipes/issues/30310
-    container "nf-core/deepvariant:1.6.1"
+    container "docker.io/google/deepvariant:1.8.0"
 
     input:
     tuple val(meta), path(input), path(index), path(intervals)
@@ -15,11 +15,11 @@ process DEEPVARIANT_RUNDEEPVARIANT {
     tuple val(meta5), path(par_bed)
 
     output:
-    tuple val(meta), path("${prefix}.vcf.gz")      ,  emit: vcf
-    tuple val(meta), path("${prefix}.vcf.gz.tbi")  ,  emit: vcf_tbi
-    tuple val(meta), path("${prefix}.g.vcf.gz")    ,  emit: gvcf
-    tuple val(meta), path("${prefix}.g.vcf.gz.tbi"),  emit: gvcf_tbi
-    path "versions.yml"                            ,  emit: versions
+    tuple val(meta), path("${prefix}.vcf.gz")      , emit: vcf
+    tuple val(meta), path("${prefix}.vcf.gz.tbi")  , emit: vcf_tbi
+    tuple val(meta), path("${prefix}.g.vcf.gz")    , emit: gvcf
+    tuple val(meta), path("${prefix}.g.vcf.gz.tbi"), emit: gvcf_tbi
+    path "versions.yml"                            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,9 +33,6 @@ process DEEPVARIANT_RUNDEEPVARIANT {
     prefix = task.ext.prefix ?: "${meta.id}"
     def regions = intervals ? "--regions=${intervals}" : ""
     def par_regions = par_bed ? "--par_regions_bed=${par_bed}" : ""
-    // WARN https://github.com/nf-core/modules/pull/5801#issuecomment-2194293755
-    // FIXME Revert this on next version bump
-    def VERSION = '1.6.1'
 
     """
     /opt/deepvariant/bin/run_deepvariant \\
@@ -51,7 +48,7 @@ process DEEPVARIANT_RUNDEEPVARIANT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        deepvariant: $VERSION
+        deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
     END_VERSIONS
     """
 
@@ -61,9 +58,6 @@ process DEEPVARIANT_RUNDEEPVARIANT {
         error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     prefix = task.ext.prefix ?: "${meta.id}"
-    // WARN https://github.com/nf-core/modules/pull/5801#issuecomment-2194293755
-    // FIXME Revert this on next version bump
-    def VERSION = '1.6.1'
     """
     touch ${prefix}.vcf.gz
     touch ${prefix}.vcf.gz.tbi
@@ -72,7 +66,7 @@ process DEEPVARIANT_RUNDEEPVARIANT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        deepvariant: $VERSION
+        deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap
index 1ec351ee..8e836336 100644
--- a/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap
+++ b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0"
+                        "test_out.vcf.gz:md5,cf14200d683c17a6e433bb076d487fee"
                     ]
                 ],
                 "1": [
@@ -17,7 +17,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21"
+                        "test_out.vcf.gz.tbi:md5,e9bcd1d1f5280e0d76ed8fd31f27bd59"
                     ]
                 ],
                 "2": [
@@ -26,7 +26,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a"
+                        "test_out.g.vcf.gz:md5,6251a87945e530ca61a989d7187d89dc"
                     ]
                 ],
                 "3": [
@@ -35,11 +35,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d"
+                        "test_out.g.vcf.gz.tbi:md5,32ca0d6713b96ed4ce07c79421bb04a9"
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
+                    "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01"
                 ],
                 "gvcf": [
                     [
@@ -47,7 +47,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a"
+                        "test_out.g.vcf.gz:md5,6251a87945e530ca61a989d7187d89dc"
                     ]
                 ],
                 "gvcf_tbi": [
@@ -56,7 +56,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d"
+                        "test_out.g.vcf.gz.tbi:md5,32ca0d6713b96ed4ce07c79421bb04a9"
                     ]
                 ],
                 "vcf": [
@@ -65,7 +65,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0"
+                        "test_out.vcf.gz:md5,cf14200d683c17a6e433bb076d487fee"
                     ]
                 ],
                 "vcf_tbi": [
@@ -74,19 +74,19 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21"
+                        "test_out.vcf.gz.tbi:md5,e9bcd1d1f5280e0d76ed8fd31f27bd59"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
+                    "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-08-29T11:36:27.325363"
+        "timestamp": "2025-01-14T08:16:22.036932742"
     },
     "homo_sapiens - [bam, bai] - fasta - fai": {
         "content": [
@@ -97,7 +97,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0"
+                        "test_out.vcf.gz:md5,cf14200d683c17a6e433bb076d487fee"
                     ]
                 ],
                 "1": [
@@ -106,7 +106,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21"
+                        "test_out.vcf.gz.tbi:md5,e9bcd1d1f5280e0d76ed8fd31f27bd59"
                     ]
                 ],
                 "2": [
@@ -115,7 +115,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a"
+                        "test_out.g.vcf.gz:md5,6251a87945e530ca61a989d7187d89dc"
                     ]
                 ],
                 "3": [
@@ -124,11 +124,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d"
+                        "test_out.g.vcf.gz.tbi:md5,32ca0d6713b96ed4ce07c79421bb04a9"
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
+                    "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01"
                 ],
                 "gvcf": [
                     [
@@ -136,7 +136,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a"
+                        "test_out.g.vcf.gz:md5,6251a87945e530ca61a989d7187d89dc"
                     ]
                 ],
                 "gvcf_tbi": [
@@ -145,7 +145,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d"
+                        "test_out.g.vcf.gz.tbi:md5,32ca0d6713b96ed4ce07c79421bb04a9"
                     ]
                 ],
                 "vcf": [
@@ -154,7 +154,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0"
+                        "test_out.vcf.gz:md5,cf14200d683c17a6e433bb076d487fee"
                     ]
                 ],
                 "vcf_tbi": [
@@ -163,19 +163,19 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21"
+                        "test_out.vcf.gz.tbi:md5,e9bcd1d1f5280e0d76ed8fd31f27bd59"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
+                    "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-08-29T11:34:41.779153"
+        "timestamp": "2025-01-14T08:13:35.621497498"
     },
     "homo_sapiens - [cram, crai, genome_bed] - fasta - fai": {
         "content": [
@@ -186,7 +186,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0"
+                        "test_out.vcf.gz:md5,cf14200d683c17a6e433bb076d487fee"
                     ]
                 ],
                 "1": [
@@ -195,7 +195,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21"
+                        "test_out.vcf.gz.tbi:md5,e9bcd1d1f5280e0d76ed8fd31f27bd59"
                     ]
                 ],
                 "2": [
@@ -204,7 +204,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a"
+                        "test_out.g.vcf.gz:md5,6251a87945e530ca61a989d7187d89dc"
                     ]
                 ],
                 "3": [
@@ -213,11 +213,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d"
+                        "test_out.g.vcf.gz.tbi:md5,32ca0d6713b96ed4ce07c79421bb04a9"
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
+                    "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01"
                 ],
                 "gvcf": [
                     [
@@ -225,7 +225,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a"
+                        "test_out.g.vcf.gz:md5,6251a87945e530ca61a989d7187d89dc"
                     ]
                 ],
                 "gvcf_tbi": [
@@ -234,7 +234,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d"
+                        "test_out.g.vcf.gz.tbi:md5,32ca0d6713b96ed4ce07c79421bb04a9"
                     ]
                 ],
                 "vcf": [
@@ -243,7 +243,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0"
+                        "test_out.vcf.gz:md5,cf14200d683c17a6e433bb076d487fee"
                     ]
                 ],
                 "vcf_tbi": [
@@ -252,19 +252,19 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21"
+                        "test_out.vcf.gz.tbi:md5,e9bcd1d1f5280e0d76ed8fd31f27bd59"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
+                    "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-08-29T11:35:16.993129"
+        "timestamp": "2025-01-14T08:14:32.23781232"
     },
     "homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_bed": {
         "content": [
@@ -275,7 +275,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz:md5,d2e26d65dbbcea9b087ed191b5c9841c"
+                        "test_out.vcf.gz:md5,b79936a7bf53fa4ee7e5866664e37d56"
                     ]
                 ],
                 "1": [
@@ -284,7 +284,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz.tbi:md5,0801296d0356415bbf1ef8deb4ec84c3"
+                        "test_out.vcf.gz.tbi:md5,22f9f4c6c8c1faa8b129eddf32b445b8"
                     ]
                 ],
                 "2": [
@@ -293,7 +293,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz:md5,4fcaa9a8b55730d191382160c2b5bb0a"
+                        "test_out.g.vcf.gz:md5,c82ce85ed16dcabe411995c52aaffd85"
                     ]
                 ],
                 "3": [
@@ -302,11 +302,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz.tbi:md5,f468e846904733b3231ecf00ef7cd4a2"
+                        "test_out.g.vcf.gz.tbi:md5,6420a456b0507c70c8423293395c29bc"
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
+                    "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01"
                 ],
                 "gvcf": [
                     [
@@ -314,7 +314,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz:md5,4fcaa9a8b55730d191382160c2b5bb0a"
+                        "test_out.g.vcf.gz:md5,c82ce85ed16dcabe411995c52aaffd85"
                     ]
                 ],
                 "gvcf_tbi": [
@@ -323,7 +323,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.g.vcf.gz.tbi:md5,f468e846904733b3231ecf00ef7cd4a2"
+                        "test_out.g.vcf.gz.tbi:md5,6420a456b0507c70c8423293395c29bc"
                     ]
                 ],
                 "vcf": [
@@ -332,7 +332,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz:md5,d2e26d65dbbcea9b087ed191b5c9841c"
+                        "test_out.vcf.gz:md5,b79936a7bf53fa4ee7e5866664e37d56"
                     ]
                 ],
                 "vcf_tbi": [
@@ -341,18 +341,18 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_out.vcf.gz.tbi:md5,0801296d0356415bbf1ef8deb4ec84c3"
+                        "test_out.vcf.gz.tbi:md5,22f9f4c6c8c1faa8b129eddf32b445b8"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890"
+                    "versions.yml:md5,cd692ea876a00da762fd4608c9f40f01"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-08-29T11:35:52.23093"
+        "timestamp": "2025-01-14T08:15:29.680851997"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/deepvariant/vcfstatsreport/main.nf b/modules/nf-core/deepvariant/vcfstatsreport/main.nf
index 5bbf06b6..314c3d2a 100644
--- a/modules/nf-core/deepvariant/vcfstatsreport/main.nf
+++ b/modules/nf-core/deepvariant/vcfstatsreport/main.nf
@@ -5,7 +5,7 @@ process DEEPVARIANT_VCFSTATSREPORT {
     // FIXME Conda is not supported at the moment
     // BUG https://github.com/nf-core/modules/issues/1754
     // BUG https://github.com/bioconda/bioconda-recipes/issues/30310
-    container "nf-core/deepvariant:1.6.1"
+    container "docker.io/google/deepvariant:1.8.0"
 
     input:
     tuple val(meta), path(vcf)
@@ -24,10 +24,6 @@ process DEEPVARIANT_VCFSTATSREPORT {
     }
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
-    // WARN https://github.com/nf-core/modules/pull/5801#issuecomment-2194293755
-    // FIXME Revert this on next version bump
-    def VERSION = '1.6.1'
-
     """
     /opt/deepvariant/bin/vcf_stats_report \\
         --input_vcf=${vcf} \\
@@ -35,7 +31,7 @@ process DEEPVARIANT_VCFSTATSREPORT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        deepvariant: $VERSION
+        deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
     END_VERSIONS
     """
 
@@ -45,15 +41,12 @@ process DEEPVARIANT_VCFSTATSREPORT {
         error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     prefix = task.ext.prefix ?: "${meta.id}"
-    // WARN https://github.com/nf-core/modules/pull/5801#issuecomment-2194293755
-    // FIXME Revert this on next version bump
-    def VERSION = '1.6.1'
     """
     touch ${prefix}.visual_report.html
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        deepvariant: $VERSION
+        deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test.snap b/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test.snap
index 9a9ac3ce..9255ccb4 100644
--- a/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test.snap
+++ b/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ],
                 "report": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-14T08:19:35.672028563"
+        "timestamp": "2025-01-14T15:13:32.380265779"
     },
     "bcf": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ],
                 "report": [
                     [
@@ -55,15 +55,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-11T07:47:10.485269156"
+        "timestamp": "2025-01-14T15:13:11.49442341"
     },
     "vcf.gz - stub": {
         "content": [
@@ -77,7 +77,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ],
                 "report": [
                     [
@@ -88,15 +88,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-14T08:34:50.411910578"
+        "timestamp": "2025-01-14T15:13:59.468946068"
     },
     "vcf.gz": {
         "content": [
@@ -110,7 +110,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ],
                 "report": [
                     [
@@ -121,15 +121,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-11T07:47:00.438649988"
+        "timestamp": "2025-01-14T15:12:52.602536212"
     },
     "vcf": {
         "content": [
@@ -143,7 +143,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ],
                 "report": [
                     [
@@ -154,15 +154,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-11T07:44:07.427456921"
+        "timestamp": "2025-01-14T15:12:35.527450489"
     },
     "bcf - stub": {
         "content": [
@@ -176,7 +176,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ],
                 "report": [
                     [
@@ -187,15 +187,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-14T08:35:03.341417618"
+        "timestamp": "2025-01-14T15:14:13.064758768"
     },
     "bcf.gz - stub": {
         "content": [
@@ -209,7 +209,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ],
                 "report": [
                     [
@@ -220,15 +220,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-14T08:35:13.52398762"
+        "timestamp": "2025-01-14T15:14:26.7174912"
     },
     "vcf - stub": {
         "content": [
@@ -242,7 +242,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ],
                 "report": [
                     [
@@ -253,14 +253,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996"
+                    "versions.yml:md5,72414085057fedf473d874c39db9b4c1"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-14T08:34:35.977457571"
+        "timestamp": "2025-01-14T15:13:46.09138006"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/methylation/tests/main.nf.test.snap b/subworkflows/local/methylation/tests/main.nf.test.snap
index a96efcdf..f89ead2c 100644
--- a/subworkflows/local/methylation/tests/main.nf.test.snap
+++ b/subworkflows/local/methylation/tests/main.nf.test.snap
@@ -7,19 +7,19 @@
                         {
                             "id": "test"
                         },
-                        "test_modkit_pileup_1.bed.gz:md5,b980e56ca6d65d09892b069a7d51b827"
+                        "test_modkit_pileup_1.bed.gz:md5,3df4afc0f8445e05c1d125df317fbc59"
                     ],
                     [
                         {
                             "id": "test"
                         },
-                        "test_modkit_pileup_2.bed.gz:md5,32a5e2148266fefba8159d98f5f5dd87"
+                        "test_modkit_pileup_2.bed.gz:md5,c069e2c7d968217b189ad098ca3de6fe"
                     ],
                     [
                         {
                             "id": "test"
                         },
-                        "test_modkit_pileup_ungrouped.bed.gz:md5,bfeda9731d6d52508301ddf939302676"
+                        "test_modkit_pileup_ungrouped.bed.gz:md5,d1d2a2bbc8b4f525e1f1da091589b4a1"
                     ]
                 ],
                 "1": [
@@ -27,19 +27,19 @@
                         {
                             "id": "test"
                         },
-                        "test_modkit_pileup_1.bed.gz.tbi:md5,45800db86a2845fe961f536484369f61"
+                        "test_modkit_pileup_1.bed.gz.tbi:md5,dc7847cfd88fa2db0c2322dc692f1a2c"
                     ],
                     [
                         {
                             "id": "test"
                         },
-                        "test_modkit_pileup_2.bed.gz.tbi:md5,14f729ebf5ce7d265df85b21c30a67af"
+                        "test_modkit_pileup_2.bed.gz.tbi:md5,94b4986c67c80a89021f45342397c097"
                     ],
                     [
                         {
                             "id": "test"
                         },
-                        "test_modkit_pileup_ungrouped.bed.gz.tbi:md5,d08da21ae562fcc3c3361a916439c552"
+                        "test_modkit_pileup_ungrouped.bed.gz.tbi:md5,a2968c28e257f46ddfc7c1352748d7b8"
                     ]
                 ],
                 "2": [
@@ -53,19 +53,19 @@
                         {
                             "id": "test"
                         },
-                        "test_modkit_pileup_1.bed.gz:md5,b980e56ca6d65d09892b069a7d51b827"
+                        "test_modkit_pileup_1.bed.gz:md5,3df4afc0f8445e05c1d125df317fbc59"
                     ],
                     [
                         {
                             "id": "test"
                         },
-                        "test_modkit_pileup_2.bed.gz:md5,32a5e2148266fefba8159d98f5f5dd87"
+                        "test_modkit_pileup_2.bed.gz:md5,c069e2c7d968217b189ad098ca3de6fe"
                     ],
                     [
                         {
                             "id": "test"
                         },
-                        "test_modkit_pileup_ungrouped.bed.gz:md5,bfeda9731d6d52508301ddf939302676"
+                        "test_modkit_pileup_ungrouped.bed.gz:md5,d1d2a2bbc8b4f525e1f1da091589b4a1"
                     ]
                 ],
                 "tbi": [
@@ -73,19 +73,19 @@
                         {
                             "id": "test"
                         },
-                        "test_modkit_pileup_1.bed.gz.tbi:md5,45800db86a2845fe961f536484369f61"
+                        "test_modkit_pileup_1.bed.gz.tbi:md5,dc7847cfd88fa2db0c2322dc692f1a2c"
                     ],
                     [
                         {
                             "id": "test"
                         },
-                        "test_modkit_pileup_2.bed.gz.tbi:md5,14f729ebf5ce7d265df85b21c30a67af"
+                        "test_modkit_pileup_2.bed.gz.tbi:md5,94b4986c67c80a89021f45342397c097"
                     ],
                     [
                         {
                             "id": "test"
                         },
-                        "test_modkit_pileup_ungrouped.bed.gz.tbi:md5,d08da21ae562fcc3c3361a916439c552"
+                        "test_modkit_pileup_ungrouped.bed.gz.tbi:md5,a2968c28e257f46ddfc7c1352748d7b8"
                     ]
                 ],
                 "versions": [
@@ -98,9 +98,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-01T16:42:19.164909715"
+        "timestamp": "2025-01-17T10:34:48.673483384"
     },
     "1 sample - bed unphased - stub": {
         "content": [
diff --git a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap
index 04be59dd..a17b3657 100644
--- a/subworkflows/local/short_variant_calling/tests/main.nf.test.snap
+++ b/subworkflows/local/short_variant_calling/tests/main.nf.test.snap
@@ -5,19 +5,35 @@
                 "0": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz:md5,8d1b64c0eed7eb66dd3294fcbc15b4a1"
+                        "test_norm_singlesample.vcf.gz:md5,81fa9df22efb2da2ad4f6e6ac5fb04dc"
                     ]
                 ],
                 "1": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz.tbi:md5,41ab8f51ac55e08b2339feb5a6b40764"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,a9e5de75aef9a36c01b6446631de8632"
                     ]
                 ],
                 "2": [
@@ -26,7 +42,7 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
+                        "genome.bed_norm_multisample.vcf.gz:md5,70d4cfd45955fd42ac61043b52bf379a"
                     ]
                 ],
                 "3": [
@@ -35,26 +51,34 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,29d4e9660de139a2ff6e12a9f2a8ac56"
                     ]
                 ],
                 "4": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test.visual_report.html:md5,828ada93b6101047c8de4789803c726c"
+                        "test.visual_report.html:md5,47b86a3fd06ade0c046bc4be2e503e15"
                     ]
                 ],
                 "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
                 "family_bcf": [
@@ -63,7 +87,7 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
+                        "genome.bed_norm_multisample.vcf.gz:md5,70d4cfd45955fd42ac61043b52bf379a"
                     ]
                 ],
                 "family_csi": [
@@ -72,53 +96,77 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,29d4e9660de139a2ff6e12a9f2a8ac56"
                     ]
                 ],
                 "snp_calls_tbi": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz.tbi:md5,41ab8f51ac55e08b2339feb5a6b40764"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,a9e5de75aef9a36c01b6446631de8632"
                     ]
                 ],
                 "snp_calls_vcf": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz:md5,8d1b64c0eed7eb66dd3294fcbc15b4a1"
+                        "test_norm_singlesample.vcf.gz:md5,81fa9df22efb2da2ad4f6e6ac5fb04dc"
                     ]
                 ],
                 "vcfstatsreport": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test.visual_report.html:md5,828ada93b6101047c8de4789803c726c"
+                        "test.visual_report.html:md5,47b86a3fd06ade0c046bc4be2e503e15"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-21T14:31:35.224934094"
+        "timestamp": "2025-01-17T10:06:33.865402104"
     },
     "1 sample - 2 bed, fasta, fai, bed, [] - stub": {
         "content": [
@@ -126,7 +174,15 @@
                 "0": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
@@ -135,7 +191,15 @@
                 "1": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -176,7 +240,15 @@
                 "4": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -185,15 +257,15 @@
                 "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
@@ -232,7 +304,15 @@
                 "snp_calls_tbi": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -241,7 +321,15 @@
                 "snp_calls_vcf": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
@@ -250,7 +338,15 @@
                 "vcfstatsreport": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -259,15 +355,15 @@
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
@@ -275,9 +371,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-21T14:34:35.379604763"
+        "timestamp": "2025-01-17T10:10:20.313600329"
     },
     "1 sample - 1 bed, fasta, fai, bed, []": {
         "content": [
@@ -285,19 +381,35 @@
                 "0": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz:md5,8d1b64c0eed7eb66dd3294fcbc15b4a1"
+                        "test_norm_singlesample.vcf.gz:md5,81fa9df22efb2da2ad4f6e6ac5fb04dc"
                     ]
                 ],
                 "1": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz.tbi:md5,41ab8f51ac55e08b2339feb5a6b40764"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,a9e5de75aef9a36c01b6446631de8632"
                     ]
                 ],
                 "2": [
@@ -306,7 +418,7 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
+                        "genome.bed_norm_multisample.vcf.gz:md5,70d4cfd45955fd42ac61043b52bf379a"
                     ]
                 ],
                 "3": [
@@ -315,26 +427,34 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,29d4e9660de139a2ff6e12a9f2a8ac56"
                     ]
                 ],
                 "4": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test.visual_report.html:md5,828ada93b6101047c8de4789803c726c"
+                        "test.visual_report.html:md5,47b86a3fd06ade0c046bc4be2e503e15"
                     ]
                 ],
                 "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
                 "family_bcf": [
@@ -343,7 +463,7 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
+                        "genome.bed_norm_multisample.vcf.gz:md5,70d4cfd45955fd42ac61043b52bf379a"
                     ]
                 ],
                 "family_csi": [
@@ -352,53 +472,77 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,29d4e9660de139a2ff6e12a9f2a8ac56"
                     ]
                 ],
                 "snp_calls_tbi": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz.tbi:md5,41ab8f51ac55e08b2339feb5a6b40764"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,a9e5de75aef9a36c01b6446631de8632"
                     ]
                 ],
                 "snp_calls_vcf": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz:md5,8d1b64c0eed7eb66dd3294fcbc15b4a1"
+                        "test_norm_singlesample.vcf.gz:md5,81fa9df22efb2da2ad4f6e6ac5fb04dc"
                     ]
                 ],
                 "vcfstatsreport": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test.visual_report.html:md5,828ada93b6101047c8de4789803c726c"
+                        "test.visual_report.html:md5,47b86a3fd06ade0c046bc4be2e503e15"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-21T14:32:05.96601253"
+        "timestamp": "2025-01-17T10:07:11.474745958"
     },
     "2 samples - 2 bed, fasta, fai, bed, par_bed": {
         "content": [
@@ -406,33 +550,49 @@
                 "0": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz:md5,f8e492c9c4d6e0cb027b300bb3f7155a"
+                        "test_norm_singlesample.vcf.gz:md5,1ee776e8f6c463f0cba72b6a6f2781ab"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "test2_norm_singlesample.vcf.gz:md5,0e42833e64e0f427ca09259e17e2765b"
+                        "test2_norm_singlesample.vcf.gz:md5,d683ca03a1cc5a66735ff9867d8fd252"
                     ]
                 ],
                 "1": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz.tbi:md5,f1d5f7e2321e7f0534d251c12b373221"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,a0561a617b167510dea4a403b28486eb"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "test2_norm_singlesample.vcf.gz.tbi:md5,2c4354a182ae1f4ad94f056b2fbf62a8"
+                        "test2_norm_singlesample.vcf.gz.tbi:md5,a0561a617b167510dea4a403b28486eb"
                     ]
                 ],
                 "2": [
@@ -441,14 +601,14 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,ce3866081a0bb6d9bd0df30dd3361213"
+                        "genome.bed_norm_multisample.vcf.gz:md5,662474da5112a49599ce1a501ad4f53b"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
                             "family_id": null
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,ce3866081a0bb6d9bd0df30dd3361213"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,662474da5112a49599ce1a501ad4f53b"
                     ]
                 ],
                 "3": [
@@ -457,35 +617,49 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,95eecbb89b9a60ecebc292e36ab4ebcf"
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,6bd1972ab098c63b5a061d7dfea7d8dd"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
                             "family_id": null
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,95eecbb89b9a60ecebc292e36ab4ebcf"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,6bd1972ab098c63b5a061d7dfea7d8dd"
                     ]
                 ],
                 "4": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test.visual_report.html:md5,316443518dbcf50923d09b07ec39a9f9"
+                        "test.visual_report.html:md5,ecc6c8c355197d91cb46fa890e82e961"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "test2.visual_report.html:md5,3358ec9541a51f43ab77cc79a8ed2f23"
+                        "test2.visual_report.html:md5,b4952fa73d698de9e777ee1143b5ebe2"
                     ]
                 ],
                 "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
@@ -494,12 +668,6 @@
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
@@ -509,14 +677,14 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,ce3866081a0bb6d9bd0df30dd3361213"
+                        "genome.bed_norm_multisample.vcf.gz:md5,662474da5112a49599ce1a501ad4f53b"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
                             "family_id": null
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,ce3866081a0bb6d9bd0df30dd3361213"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,662474da5112a49599ce1a501ad4f53b"
                     ]
                 ],
                 "family_csi": [
@@ -525,67 +693,97 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,95eecbb89b9a60ecebc292e36ab4ebcf"
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,6bd1972ab098c63b5a061d7dfea7d8dd"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
                             "family_id": null
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,95eecbb89b9a60ecebc292e36ab4ebcf"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,6bd1972ab098c63b5a061d7dfea7d8dd"
                     ]
                 ],
                 "snp_calls_tbi": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz.tbi:md5,f1d5f7e2321e7f0534d251c12b373221"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,a0561a617b167510dea4a403b28486eb"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "test2_norm_singlesample.vcf.gz.tbi:md5,2c4354a182ae1f4ad94f056b2fbf62a8"
+                        "test2_norm_singlesample.vcf.gz.tbi:md5,a0561a617b167510dea4a403b28486eb"
                     ]
                 ],
                 "snp_calls_vcf": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz:md5,f8e492c9c4d6e0cb027b300bb3f7155a"
+                        "test_norm_singlesample.vcf.gz:md5,1ee776e8f6c463f0cba72b6a6f2781ab"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "test2_norm_singlesample.vcf.gz:md5,0e42833e64e0f427ca09259e17e2765b"
+                        "test2_norm_singlesample.vcf.gz:md5,d683ca03a1cc5a66735ff9867d8fd252"
                     ]
                 ],
                 "vcfstatsreport": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test.visual_report.html:md5,316443518dbcf50923d09b07ec39a9f9"
+                        "test.visual_report.html:md5,ecc6c8c355197d91cb46fa890e82e961"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "test2.visual_report.html:md5,3358ec9541a51f43ab77cc79a8ed2f23"
+                        "test2.visual_report.html:md5,b4952fa73d698de9e777ee1143b5ebe2"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
@@ -594,12 +792,6 @@
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
@@ -607,9 +799,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-21T14:33:48.773081634"
+        "timestamp": "2025-01-17T10:09:19.566542982"
     },
     "2 samples - 2 bed, fasta, fai, bed, [] - stub": {
         "content": [
@@ -617,7 +809,15 @@
                 "0": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
@@ -633,7 +833,15 @@
                 "1": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -681,7 +889,15 @@
                 "4": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -697,6 +913,12 @@
                 "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
@@ -705,12 +927,6 @@
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
@@ -749,7 +965,15 @@
                 "snp_calls_tbi": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -765,7 +989,15 @@
                 "snp_calls_vcf": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
@@ -781,7 +1013,15 @@
                 "vcfstatsreport": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -797,6 +1037,12 @@
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
@@ -805,12 +1051,6 @@
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
@@ -818,9 +1058,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-21T14:34:48.741504128"
+        "timestamp": "2025-01-17T10:10:38.60531482"
     },
     "2 samples - 2 bed, fasta, fai, bed, par_bed - stub": {
         "content": [
@@ -828,7 +1068,15 @@
                 "0": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
@@ -844,7 +1092,15 @@
                 "1": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -892,7 +1148,15 @@
                 "4": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -908,6 +1172,12 @@
                 "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
@@ -916,12 +1186,6 @@
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
@@ -960,7 +1224,15 @@
                 "snp_calls_tbi": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -976,7 +1248,15 @@
                 "snp_calls_vcf": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
@@ -992,7 +1272,15 @@
                 "vcfstatsreport": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1008,6 +1296,12 @@
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
@@ -1016,12 +1310,6 @@
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
@@ -1029,9 +1317,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-21T14:35:02.231722564"
+        "timestamp": "2025-01-17T10:10:57.115636413"
     },
     "1 sample - 1 bed, fasta, fai, bed, [] - stub": {
         "content": [
@@ -1039,7 +1327,15 @@
                 "0": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
@@ -1048,7 +1344,15 @@
                 "1": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1075,7 +1379,15 @@
                 "4": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1083,12 +1395,12 @@
                 ],
                 "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
                 "family_bcf": [
@@ -1112,7 +1424,15 @@
                 "snp_calls_tbi": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1121,7 +1441,15 @@
                 "snp_calls_vcf": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
@@ -1130,7 +1458,15 @@
                 "vcfstatsreport": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1138,21 +1474,21 @@
                 ],
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-21T14:34:22.842191526"
+        "timestamp": "2025-01-17T10:10:03.862445879"
     },
     "1 sample - no bed, fasta, fai, [], []": {
         "content": [
@@ -1160,19 +1496,35 @@
                 "0": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz:md5,8d1b64c0eed7eb66dd3294fcbc15b4a1"
+                        "test_norm_singlesample.vcf.gz:md5,81fa9df22efb2da2ad4f6e6ac5fb04dc"
                     ]
                 ],
                 "1": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
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+                        "test_norm_singlesample.vcf.gz.tbi:md5,a9e5de75aef9a36c01b6446631de8632"
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@@ -1183,7 +1535,7 @@
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-                        "[]_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
+                        "[]_norm_multisample.vcf.gz:md5,70d4cfd45955fd42ac61043b52bf379a"
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@@ -1194,26 +1546,34 @@
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-                        "[]_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                        "[]_norm_multisample.vcf.gz.csi:md5,29d4e9660de139a2ff6e12a9f2a8ac56"
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                 "4": [
                     [
                         {
-                            "id": "test",
+                            "id": [
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+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
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                             "single_end": false
                         },
-                        "test.visual_report.html:md5,828ada93b6101047c8de4789803c726c"
+                        "test.visual_report.html:md5,47b86a3fd06ade0c046bc4be2e503e15"
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                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
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                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
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                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
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                 "family_bcf": [
@@ -1224,7 +1584,7 @@
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-                        "[]_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
+                        "[]_norm_multisample.vcf.gz:md5,70d4cfd45955fd42ac61043b52bf379a"
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                 "family_csi": [
@@ -1235,53 +1595,77 @@
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-                        "[]_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                        "[]_norm_multisample.vcf.gz.csi:md5,29d4e9660de139a2ff6e12a9f2a8ac56"
                     ]
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                 "snp_calls_tbi": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
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                             "single_end": false
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+                        "test_norm_singlesample.vcf.gz.tbi:md5,a9e5de75aef9a36c01b6446631de8632"
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                 "snp_calls_vcf": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
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                             "single_end": false
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+                        "test_norm_singlesample.vcf.gz:md5,81fa9df22efb2da2ad4f6e6ac5fb04dc"
                     ]
                 ],
                 "vcfstatsreport": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
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+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
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                             "single_end": false
                         },
-                        "test.visual_report.html:md5,828ada93b6101047c8de4789803c726c"
+                        "test.visual_report.html:md5,47b86a3fd06ade0c046bc4be2e503e15"
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                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
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                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
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         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-21T14:31:04.363638442"
+        "timestamp": "2025-01-17T10:05:56.604289136"
     },
     "1 sample - 2 bed, fasta, fai, bed, []": {
         "content": [
@@ -1289,19 +1673,35 @@
                 "0": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
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+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz:md5,f8e492c9c4d6e0cb027b300bb3f7155a"
+                        "test_norm_singlesample.vcf.gz:md5,1ee776e8f6c463f0cba72b6a6f2781ab"
                     ]
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                 "1": [
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                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
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+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
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                         },
-                        "test_norm_singlesample.vcf.gz.tbi:md5,f1d5f7e2321e7f0534d251c12b373221"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,a0561a617b167510dea4a403b28486eb"
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                 "2": [
@@ -1310,14 +1710,14 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
+                        "genome.bed_norm_multisample.vcf.gz:md5,70d4cfd45955fd42ac61043b52bf379a"
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                     [
                         {
                             "id": "genome.multi_intervals.bed",
                             "family_id": null
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-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,70d4cfd45955fd42ac61043b52bf379a"
                     ]
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                 "3": [
@@ -1326,37 +1726,45 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,29d4e9660de139a2ff6e12a9f2a8ac56"
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                         {
                             "id": "genome.multi_intervals.bed",
                             "family_id": null
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-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,29d4e9660de139a2ff6e12a9f2a8ac56"
                     ]
                 ],
                 "4": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
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+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test.visual_report.html:md5,316443518dbcf50923d09b07ec39a9f9"
+                        "test.visual_report.html:md5,ecc6c8c355197d91cb46fa890e82e961"
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                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
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                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
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                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
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@@ -1366,14 +1774,14 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
+                        "genome.bed_norm_multisample.vcf.gz:md5,70d4cfd45955fd42ac61043b52bf379a"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
                             "family_id": null
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,5d1828b40d43a2a18e30b1dffffd99b0"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,70d4cfd45955fd42ac61043b52bf379a"
                     ]
                 ],
                 "family_csi": [
@@ -1382,55 +1790,79 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,29d4e9660de139a2ff6e12a9f2a8ac56"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
                             "family_id": null
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,83a0cecdb72c82ae0f5fc56f1426f5c0"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,29d4e9660de139a2ff6e12a9f2a8ac56"
                     ]
                 ],
                 "snp_calls_tbi": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz.tbi:md5,f1d5f7e2321e7f0534d251c12b373221"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,a0561a617b167510dea4a403b28486eb"
                     ]
                 ],
                 "snp_calls_vcf": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz:md5,f8e492c9c4d6e0cb027b300bb3f7155a"
+                        "test_norm_singlesample.vcf.gz:md5,1ee776e8f6c463f0cba72b6a6f2781ab"
                     ]
                 ],
                 "vcfstatsreport": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test.visual_report.html:md5,316443518dbcf50923d09b07ec39a9f9"
+                        "test.visual_report.html:md5,ecc6c8c355197d91cb46fa890e82e961"
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                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
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                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
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                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
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@@ -1438,9 +1870,9 @@
         ],
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             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-21T14:32:38.48715039"
+        "timestamp": "2025-01-17T10:07:51.929233722"
     },
     "2 samples - 2 bed, fasta, fai, bed, []": {
         "content": [
@@ -1448,33 +1880,49 @@
                 "0": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz:md5,f8e492c9c4d6e0cb027b300bb3f7155a"
+                        "test_norm_singlesample.vcf.gz:md5,1ee776e8f6c463f0cba72b6a6f2781ab"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "test2_norm_singlesample.vcf.gz:md5,0e42833e64e0f427ca09259e17e2765b"
+                        "test2_norm_singlesample.vcf.gz:md5,d683ca03a1cc5a66735ff9867d8fd252"
                     ]
                 ],
                 "1": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz.tbi:md5,f1d5f7e2321e7f0534d251c12b373221"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,a0561a617b167510dea4a403b28486eb"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "test2_norm_singlesample.vcf.gz.tbi:md5,2c4354a182ae1f4ad94f056b2fbf62a8"
+                        "test2_norm_singlesample.vcf.gz.tbi:md5,a0561a617b167510dea4a403b28486eb"
                     ]
                 ],
                 "2": [
@@ -1483,14 +1931,14 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,ce3866081a0bb6d9bd0df30dd3361213"
+                        "genome.bed_norm_multisample.vcf.gz:md5,662474da5112a49599ce1a501ad4f53b"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
                             "family_id": null
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,ce3866081a0bb6d9bd0df30dd3361213"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,662474da5112a49599ce1a501ad4f53b"
                     ]
                 ],
                 "3": [
@@ -1499,35 +1947,49 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,95eecbb89b9a60ecebc292e36ab4ebcf"
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,6bd1972ab098c63b5a061d7dfea7d8dd"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
                             "family_id": null
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,95eecbb89b9a60ecebc292e36ab4ebcf"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,6bd1972ab098c63b5a061d7dfea7d8dd"
                     ]
                 ],
                 "4": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test.visual_report.html:md5,316443518dbcf50923d09b07ec39a9f9"
+                        "test.visual_report.html:md5,ecc6c8c355197d91cb46fa890e82e961"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "test2.visual_report.html:md5,3358ec9541a51f43ab77cc79a8ed2f23"
+                        "test2.visual_report.html:md5,b4952fa73d698de9e777ee1143b5ebe2"
                     ]
                 ],
                 "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
@@ -1536,12 +1998,6 @@
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
@@ -1551,14 +2007,14 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz:md5,ce3866081a0bb6d9bd0df30dd3361213"
+                        "genome.bed_norm_multisample.vcf.gz:md5,662474da5112a49599ce1a501ad4f53b"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
                             "family_id": null
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,ce3866081a0bb6d9bd0df30dd3361213"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz:md5,662474da5112a49599ce1a501ad4f53b"
                     ]
                 ],
                 "family_csi": [
@@ -1567,67 +2023,97 @@
                             "id": "genome.bed",
                             "family_id": null
                         },
-                        "genome.bed_norm_multisample.vcf.gz.csi:md5,95eecbb89b9a60ecebc292e36ab4ebcf"
+                        "genome.bed_norm_multisample.vcf.gz.csi:md5,6bd1972ab098c63b5a061d7dfea7d8dd"
                     ],
                     [
                         {
                             "id": "genome.multi_intervals.bed",
                             "family_id": null
                         },
-                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,95eecbb89b9a60ecebc292e36ab4ebcf"
+                        "genome.multi_intervals.bed_norm_multisample.vcf.gz.csi:md5,6bd1972ab098c63b5a061d7dfea7d8dd"
                     ]
                 ],
                 "snp_calls_tbi": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz.tbi:md5,f1d5f7e2321e7f0534d251c12b373221"
+                        "test_norm_singlesample.vcf.gz.tbi:md5,a0561a617b167510dea4a403b28486eb"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "test2_norm_singlesample.vcf.gz.tbi:md5,2c4354a182ae1f4ad94f056b2fbf62a8"
+                        "test2_norm_singlesample.vcf.gz.tbi:md5,a0561a617b167510dea4a403b28486eb"
                     ]
                 ],
                 "snp_calls_vcf": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test_norm_singlesample.vcf.gz:md5,f8e492c9c4d6e0cb027b300bb3f7155a"
+                        "test_norm_singlesample.vcf.gz:md5,1ee776e8f6c463f0cba72b6a6f2781ab"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "test2_norm_singlesample.vcf.gz:md5,0e42833e64e0f427ca09259e17e2765b"
+                        "test2_norm_singlesample.vcf.gz:md5,d683ca03a1cc5a66735ff9867d8fd252"
                     ]
                 ],
                 "vcfstatsreport": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
-                        "test.visual_report.html:md5,316443518dbcf50923d09b07ec39a9f9"
+                        "test.visual_report.html:md5,ecc6c8c355197d91cb46fa890e82e961"
                     ],
                     [
                         {
                             "id": "test2",
                             "single_end": false
                         },
-                        "test2.visual_report.html:md5,3358ec9541a51f43ab77cc79a8ed2f23"
+                        "test2.visual_report.html:md5,b4952fa73d698de9e777ee1143b5ebe2"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
@@ -1636,12 +2122,6 @@
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
@@ -1649,9 +2129,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-21T14:33:13.404225198"
+        "timestamp": "2025-01-17T10:08:35.0730723"
     },
     "1 sample - no bed, fasta, fai, [], [] - stub": {
         "content": [
@@ -1659,7 +2139,15 @@
                 "0": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
@@ -1668,7 +2156,15 @@
                 "1": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1699,7 +2195,15 @@
                 "4": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1707,12 +2211,12 @@
                 ],
                 "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
                 "family_bcf": [
@@ -1740,7 +2244,15 @@
                 "snp_calls_tbi": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1749,7 +2261,15 @@
                 "snp_calls_vcf": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
@@ -1758,7 +2278,15 @@
                 "vcfstatsreport": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1766,21 +2294,21 @@
                 ],
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-21T14:33:59.832105156"
+        "timestamp": "2025-01-17T10:09:34.385093232"
     },
     "1 sample - 1 bed, fasta, fai, [], [] - stub": {
         "content": [
@@ -1788,7 +2316,15 @@
                 "0": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
@@ -1797,7 +2333,15 @@
                 "1": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1824,7 +2368,15 @@
                 "4": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1832,12 +2384,12 @@
                 ],
                 "5": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ],
                 "family_bcf": [
@@ -1861,7 +2413,15 @@
                 "snp_calls_tbi": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1870,7 +2430,15 @@
                 "snp_calls_vcf": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test_norm_singlesample.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
@@ -1879,7 +2447,15 @@
                 "vcfstatsreport": [
                     [
                         {
-                            "id": "test",
+                            "id": [
+                                [
+                                    "nallo_pipeline_software_mqc_versions.yml:md5,6157c11eb5ced278007f6fd9953ad938",
+                                    "params_2025-01-17_09-11-16.json:md5,70938edaeb9c5b0c54f94dafda7fdc6d",
+                                    "params_2025-01-17_09-11-42.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-03.json:md5,619bb812083605baca3c11c81655e936",
+                                    "params_2025-01-17_09-12-22.json:md5,3eae523b0bcba58bb73bfa4605c445fa"
+                                ]
+                            ],
                             "single_end": false
                         },
                         "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -1887,20 +2463,20 @@
                 ],
                 "versions": [
                     "versions.yml:md5,0ca81f5e441a48c6c650a07c7045ed34",
+                    "versions.yml:md5,18c48eaab4eafaa62eff8c6dc0fb0ef8",
+                    "versions.yml:md5,4b2d155ab1b934f9d5dd1ab9292c4834",
                     "versions.yml:md5,77dbd5f16ae8b59d09563a07be6faa44",
                     "versions.yml:md5,7d9ebdfc24f293b07e70dd2d18f44022",
                     "versions.yml:md5,afe349eb9156445b91cacdcfaabcf43d",
                     "versions.yml:md5,dce103ef6b2f37c6844db8191418b9e6",
-                    "versions.yml:md5,ee687c9b68546c8138fab17f68b967c0",
-                    "versions.yml:md5,f13ae32e1e3f3d274d4b3c7097f56531",
                     "versions.yml:md5,f8e25357cdcef69ae5ee0cd801960b50"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-11-21T14:34:11.123087909"
+        "timestamp": "2025-01-17T10:09:48.998315542"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/local/snv_annotation/tests/main.nf.test.snap b/subworkflows/local/snv_annotation/tests/main.nf.test.snap
index 2973a379..10fdf073 100644
--- a/subworkflows/local/snv_annotation/tests/main.nf.test.snap
+++ b/subworkflows/local/snv_annotation/tests/main.nf.test.snap
@@ -41,13 +41,13 @@
                 "versions.yml:md5,f533675b4401f25d7dcfc9f63abeb619"
             ],
             "test_data.bed.vcf.gz.tbi",
-            "ad2f3def07bee1f4bab9cfe456dada3e",
+            "b85129ecd461179b96d97bff6f1ab309",
             "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=121, phased=false, phasedAutodetect=false]"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-10-08T11:44:29.495925133"
+        "timestamp": "2025-01-17T10:11:47.362408395"
     }
 }
\ No newline at end of file
diff --git a/tests/samplesheet.nf.test.snap b/tests/samplesheet.nf.test.snap
index 87f39e78..a50ba52e 100644
--- a/tests/samplesheet.nf.test.snap
+++ b/tests/samplesheet.nf.test.snap
@@ -73,10 +73,10 @@
                     "gawk": "5.1.0"
                 },
                 "DEEPVARIANT_RUNDEEPVARIANT": {
-                    "deepvariant": "1.6.1"
+                    "deepvariant": "1.8.0"
                 },
                 "DEEPVARIANT_VCFSTATSREPORT": {
-                    "deepvariant": "1.6.1"
+                    "deepvariant": "1.8.0"
                 },
                 "DIPCALL": {
                     "dipcall": 0.3
@@ -528,14 +528,14 @@
                 "HG002_Revio.hap2.sam.gz:md5,6d512a060c74428f7758aa51a99ae8c8",
                 "HG002_Revio.hap2.var.gz:md5,9ba9303b30730e419138e177c7d1e0c2",
                 "HG002_Revio.pair.vcf.gz:md5,1909dffa43850282fe7e5ae2b2d273a7",
-                "HG002_Revio_modkit_pileup_1.bed.gz:md5,ac9bfc455d0b697a4bd565b510c155e0",
-                "HG002_Revio_modkit_pileup_1.bed.gz.tbi:md5,5a9ac375a0ce33af002e0073635a3425",
-                "HG002_Revio_modkit_pileup_2.bed.gz:md5,b2c6c3fc27d34b7c588a4a4b3e9611b0",
-                "HG002_Revio_modkit_pileup_2.bed.gz.tbi:md5,2ad55c2f604cbdf6a784b2dd99b25cb1",
-                "HG002_Revio_modkit_pileup_ungrouped.bed.gz:md5,04ee840c02e04238b9432bc374a1afe1",
-                "HG002_Revio_modkit_pileup_ungrouped.bed.gz.tbi:md5,e1418c8075da8831a52e0cd56ceb910e",
-                "bcftools-stats-subtypes.txt:md5,2c23b13117d584b4f424c2bc56dfa4ba",
-                "bcftools_stats_indel-lengths.txt:md5,bea599c38615af6a033ea3a4436d52c5",
+                "HG002_Revio_modkit_pileup_1.bed.gz:md5,1d90dc72aea71d6c9de602cc51aa9861",
+                "HG002_Revio_modkit_pileup_1.bed.gz.tbi:md5,52170bbfdc00a08e2fb1c41d8c8ae2cf",
+                "HG002_Revio_modkit_pileup_2.bed.gz:md5,2aa5ded8734f4f1f0bc33b6579e8dbb2",
+                "HG002_Revio_modkit_pileup_2.bed.gz.tbi:md5,a0f4c0816ad6a959f622e53d14135a0b",
+                "HG002_Revio_modkit_pileup_ungrouped.bed.gz:md5,83f1077cc6de2874e57b56d4e56351ae",
+                "HG002_Revio_modkit_pileup_ungrouped.bed.gz.tbi:md5,63ea06ad5d4bc3a639cee0af0c8d56ae",
+                "bcftools-stats-subtypes.txt:md5,c9b6f7f1312db6df868853105d89fe7e",
+                "bcftools_stats_indel-lengths.txt:md5,dcaa284529d408b8d3874ffec9155bee",
                 "fastqc-status-check-heatmap.txt:md5,f98c3e5395cfd3061b3228a97ba86043",
                 "fastqc_adapter_content_plot.txt:md5,85e76640241ce1fd8e3bbf42eb3fa447",
                 "fastqc_per_base_n_content_plot.txt:md5,c9e46e2888289c319e1b9f412cb0d8e5",
@@ -552,14 +552,14 @@
                 "mosdepth_cov_dist.txt:md5,eeb7f82eb03344d26a99b6596a1c7413",
                 "mosdepth_cumcov_dist.txt:md5,eeb7f82eb03344d26a99b6596a1c7413",
                 "mosdepth_perchrom.txt:md5,53806d793d5627e60648daebb6606723",
-                "multiqc_bcftools_stats.txt:md5,09a616618fb506994ce178d32325159f",
+                "multiqc_bcftools_stats.txt:md5,bad0bfc370ee3b3326a8482e9abea662",
                 "multiqc_citations.txt:md5,a27affce20d456d20ed387097a4f0350",
                 "multiqc_fastqc.txt:md5,8c0330b85e73f68610d35dd71f234cce",
-                "multiqc_general_stats.txt:md5,8ead46d7d8d14fc8892789a40193646f",
-                "multiqc_whatshap_phased_bp_plot.txt:md5,41dcd2951f7a6f925f64519491c18d45",
-                "multiqc_whatshap_stats.txt:md5,c8c212ecc6fbf6803f8de87f2395363f",
+                "multiqc_general_stats.txt:md5,a2d41ee520ee9cc384abf316e24551c8",
+                "multiqc_whatshap_phased_bp_plot.txt:md5,0fbe8cfe2dc10088005c2d8aba0b289a",
+                "multiqc_whatshap_stats.txt:md5,3ce08de7d7c28da214083b6321067a69",
                 "somalier_stats.txt:md5,150fa6b9c197c539947168c11d2115f9",
-                "whatshap-stats-table.txt:md5,c89df1fe6abe77dcbfce8e443c1cecde",
+                "whatshap-stats-table.txt:md5,8cc1d8ade38cf3ae084b85d24d8e2f31",
                 "FAM.ped:md5,bd5cec27ba7337a85cf98e787131e2b5",
                 "HG002_Revio_cramino_aligned_phased.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
                 "HG002_Revio_cramino_aligned.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
@@ -568,11 +568,11 @@
                 "HG002_Revio.mosdepth.summary.txt:md5,35c51f1ad9d2856d1e6446205f19a8e3",
                 "HG002_Revio.regions.bed.gz:md5,e051f64c7a780d67ea6727a327dd4281",
                 "HG002_Revio.regions.bed.gz.csi:md5,026eef1c69fb4aa3a1687463fe2088ab",
-                "HG002_Revio_stats.blocks.tsv:md5,e73960d863a78848498499480ea9937f",
-                "HG002_Revio_stats.stats.tsv:md5,cffa4a500350b2227ab40bbbe428e9ef",
+                "HG002_Revio_stats.blocks.tsv:md5,dc631306f4ff70ff0352994b2a975917",
+                "HG002_Revio_stats.stats.tsv:md5,6adb96784c82826928ebfc4f4726a35d",
                 "HG002_Revio_hificnv.copynum.bedgraph:md5,517bc59c1b235490c79aa8319437b033",
                 "HG002_Revio_hificnv.depth.bw:md5,70211e34c58cd83f6c9c6f2a8bda4a3b",
-                "HG002_Revio_hificnv.maf.bw:md5,8340a82b7b3da36383511631ed21066c"
+                "HG002_Revio_hificnv.maf.bw:md5,cffee4ce0734c1c6eae507c0f80c4a4a"
             ],
             [
                 [
@@ -623,15 +623,15 @@
                 ],
                 [
                     "FAM_snv_annotated_ranked.vcf.gz",
-                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=103, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=113, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "FAM_snvs_annotated_ranked_filtered.vcf.gz",
-                    "VcfFile [chromosomes=[chr16], sampleCount=1, variantCount=54, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chr16], sampleCount=1, variantCount=64, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "HG002_Revio_snvs_annotated_ranked.vcf.gz",
-                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=100, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=113, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "FAM_svs_cnvs_merged_annotated_ranked.vcf.gz",
@@ -673,6 +673,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-16T14:54:25.233161302"
+        "timestamp": "2025-01-17T10:14:03.463029732"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/samplesheet_multisample_bam.nf.test.snap b/tests/samplesheet_multisample_bam.nf.test.snap
index 1c6743bd..db7e5f0a 100644
--- a/tests/samplesheet_multisample_bam.nf.test.snap
+++ b/tests/samplesheet_multisample_bam.nf.test.snap
@@ -73,10 +73,10 @@
                     "gawk": "5.1.0"
                 },
                 "DEEPVARIANT_RUNDEEPVARIANT": {
-                    "deepvariant": "1.6.1"
+                    "deepvariant": "1.8.0"
                 },
                 "DEEPVARIANT_VCFSTATSREPORT": {
-                    "deepvariant": "1.6.1"
+                    "deepvariant": "1.8.0"
                 },
                 "DIPCALL": {
                     "dipcall": 0.3
@@ -640,18 +640,18 @@
                 "HG002_Revio_B.pair.vcf.gz:md5,676492865a9d4765835638d52651af73",
                 "HG002_Revio_A_modkit_pileup_1.bed.gz:md5,7af3b6246d0c007aec686714b96a0f7f",
                 "HG002_Revio_A_modkit_pileup_1.bed.gz.tbi:md5,b7083ebf6ba176ed5a472ad653c5be27",
-                "HG002_Revio_A_modkit_pileup_2.bed.gz:md5,a2e1291b468361412899cf811022fe72",
-                "HG002_Revio_A_modkit_pileup_2.bed.gz.tbi:md5,d1c192d65d8fa8cbb8ffa2e545282fde",
-                "HG002_Revio_A_modkit_pileup_ungrouped.bed.gz:md5,9a077eb24b17d6511e849c5b533cda64",
-                "HG002_Revio_A_modkit_pileup_ungrouped.bed.gz.tbi:md5,f569a923cc5204df5dc495354ab83a13",
+                "HG002_Revio_A_modkit_pileup_2.bed.gz:md5,98e42ec905d8af26046862618ca0823e",
+                "HG002_Revio_A_modkit_pileup_2.bed.gz.tbi:md5,faf05a4719d377272707695c0e4ec00c",
+                "HG002_Revio_A_modkit_pileup_ungrouped.bed.gz:md5,df4ab49fa137c8c579600a840b80dddb",
+                "HG002_Revio_A_modkit_pileup_ungrouped.bed.gz.tbi:md5,a2ecffb2ab8c47f83bf69e594d7f2e11",
                 "HG002_Revio_B_modkit_pileup_1.bed.gz:md5,d8c15e30192ce878d17dffcc0981658a",
                 "HG002_Revio_B_modkit_pileup_1.bed.gz.tbi:md5,2d400d38de3f45871bffac0ca0d3d7d3",
-                "HG002_Revio_B_modkit_pileup_2.bed.gz:md5,a2e1291b468361412899cf811022fe72",
-                "HG002_Revio_B_modkit_pileup_2.bed.gz.tbi:md5,d1c192d65d8fa8cbb8ffa2e545282fde",
-                "HG002_Revio_B_modkit_pileup_ungrouped.bed.gz:md5,49d9380eb739081b7a0b4dfa7756d09c",
-                "HG002_Revio_B_modkit_pileup_ungrouped.bed.gz.tbi:md5,f569a923cc5204df5dc495354ab83a13",
-                "bcftools-stats-subtypes.txt:md5,5b9c985c35950dfb8cd7827fc8d524c4",
-                "bcftools_stats_indel-lengths.txt:md5,9272a5340f808c3f5874f1b2fd18da6c",
+                "HG002_Revio_B_modkit_pileup_2.bed.gz:md5,98e42ec905d8af26046862618ca0823e",
+                "HG002_Revio_B_modkit_pileup_2.bed.gz.tbi:md5,faf05a4719d377272707695c0e4ec00c",
+                "HG002_Revio_B_modkit_pileup_ungrouped.bed.gz:md5,edba4bf3eb5f495de0abc644250f2a86",
+                "HG002_Revio_B_modkit_pileup_ungrouped.bed.gz.tbi:md5,e92aa5ffec112c289999ea1f641f957f",
+                "bcftools-stats-subtypes.txt:md5,a4da6fbf393643d7b5806c0ce0baf1b8",
+                "bcftools_stats_indel-lengths.txt:md5,ae0daf7a16f19b42c9db7b70bb8f03e8",
                 "fastqc-status-check-heatmap.txt:md5,20c6520b895e05df6cfeab492819e94a",
                 "fastqc_adapter_content_plot.txt:md5,8f9e7b3e1e31caeb58b0fbf31624ea53",
                 "fastqc_overrepresented_sequences_plot.txt:md5,9b021bffa0a2d100fdbe637fa7c40a62",
@@ -669,21 +669,21 @@
                 "mosdepth_cov_dist.txt:md5,c53933e0b572d115ecd35a5adb3e0a04",
                 "mosdepth_cumcov_dist.txt:md5,c53933e0b572d115ecd35a5adb3e0a04",
                 "mosdepth_perchrom.txt:md5,9fd9c40c7a6be06a338f2039a5d91fb8",
-                "multiqc_bcftools_stats.txt:md5,dbbc176792fbf2845547dfdcd39fc208",
+                "multiqc_bcftools_stats.txt:md5,e7fd1b0faf6aeeb3e309c9a564d7ce2e",
                 "multiqc_citations.txt:md5,a27affce20d456d20ed387097a4f0350",
                 "multiqc_fastqc.txt:md5,e466de366de86998b84ba6c25aafafd6",
-                "multiqc_general_stats.txt:md5,d1bfae61713bed6068386db5cb92cde9",
-                "multiqc_whatshap_phased_bp_plot.txt:md5,d70d629693c3229c37750440636c0a90",
-                "multiqc_whatshap_stats.txt:md5,96447de4e14a9b4a570c24513de64970",
+                "multiqc_general_stats.txt:md5,4af1f720701c74f79efcda18fa277fd4",
+                "multiqc_whatshap_phased_bp_plot.txt:md5,00a70348333fb7e3d78b4273ccc5f68d",
+                "multiqc_whatshap_stats.txt:md5,4ab74dc26987ff1f1080172844435935",
                 "somalier_stats.txt:md5,5f523bdaa8f6b6bf1581694564521891",
-                "whatshap-stats-table.txt:md5,862f90185133703811c955c45f5750fa",
+                "whatshap-stats-table.txt:md5,cf1e1b8c6d93d22787242466d551109c",
                 "FAM.ped:md5,24d8694d580f782ed77d4d1b5c6f6fb4",
-                "HG002_Revio_A_phased.blocks.tsv:md5,27ce044ba581da15ef838cbb343a64cf",
-                "HG002_Revio_A_phased.stats.tsv:md5,58ae1b01d01b922d022ad025a81f1026",
-                "HG002_Revio_A_phased.summary.tsv:md5,714496292cba53669081ac3be3078c28",
-                "HG002_Revio_B_phased.blocks.tsv:md5,07e7c8ebfff969db8d16890aa6a4766b",
-                "HG002_Revio_B_phased.stats.tsv:md5,f5d83609c032dee6d3056559a5994b15",
-                "HG002_Revio_B_phased.summary.tsv:md5,4acacb1a89a27ddf4c4ca49c49899245",
+                "HG002_Revio_A_phased.blocks.tsv:md5,91c00d4fc8ec729ad8ddbe9b2d6b63c5",
+                "HG002_Revio_A_phased.stats.tsv:md5,08cadde9270278da6ed3fd3b481ad9d9",
+                "HG002_Revio_A_phased.summary.tsv:md5,12dcd1637e2d7c73ef9b998cb00b3929",
+                "HG002_Revio_B_phased.blocks.tsv:md5,e72279521f04bc37fd4fbabf8e2a8503",
+                "HG002_Revio_B_phased.stats.tsv:md5,25095531c029150ccc12aeba12795985",
+                "HG002_Revio_B_phased.summary.tsv:md5,bd05af97ea6e74bc216bc9445f55faf6",
                 "HG002_Revio_A_cramino_aligned_phased.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
                 "HG002_Revio_B_cramino_aligned_phased.arrow:md5,544a6513e7604d6425a664855212eced",
                 "HG002_Revio_A_cramino_aligned.arrow:md5,72df2934ff8aa7e1bf8cf8a4881a0d2a",
@@ -698,16 +698,16 @@
                 "HG002_Revio_B.mosdepth.summary.txt:md5,191877ae5228e7880276585557a7b218",
                 "HG002_Revio_B.regions.bed.gz:md5,9c4c037139c752c60385d3c0b905af7f",
                 "HG002_Revio_B.regions.bed.gz.csi:md5,d0640255d527e36655281f64e184b02c",
-                "HG002_Revio_A_stats.blocks.tsv:md5,846f21bc3d8dd9e9d68cb00d63484ec2",
-                "HG002_Revio_A_stats.stats.tsv:md5,1504949804b510cc57d20e2c78fb7294",
-                "HG002_Revio_B_stats.blocks.tsv:md5,df646f43e67f37df5a9ec148e431d4c3",
-                "HG002_Revio_B_stats.stats.tsv:md5,40994b57e7c0bafee411bc2ad6ffb79d",
+                "HG002_Revio_A_stats.blocks.tsv:md5,62a91b634efa68a74e42141b6312b145",
+                "HG002_Revio_A_stats.stats.tsv:md5,f115ed22f863f2da51151f160ce1bcee",
+                "HG002_Revio_B_stats.blocks.tsv:md5,644b6fa58d13ff899ec3792988cca4f9",
+                "HG002_Revio_B_stats.stats.tsv:md5,e224a5892ce56e0152fcc886340262e5",
                 "HG002_Revio_A_hificnv.copynum.bedgraph:md5,517bc59c1b235490c79aa8319437b033",
                 "HG002_Revio_A_hificnv.depth.bw:md5,70211e34c58cd83f6c9c6f2a8bda4a3b",
-                "HG002_Revio_A_hificnv.maf.bw:md5,8340a82b7b3da36383511631ed21066c",
+                "HG002_Revio_A_hificnv.maf.bw:md5,cffee4ce0734c1c6eae507c0f80c4a4a",
                 "HG002_Revio_B_hificnv.copynum.bedgraph:md5,42095da173e46804977bbbecc2fda3aa",
                 "HG002_Revio_B_hificnv.depth.bw:md5,f49416b122b334f3defe7bee6dd60d48",
-                "HG002_Revio_B_hificnv.maf.bw:md5,186a7500b0c039650f726480e44b621d"
+                "HG002_Revio_B_hificnv.maf.bw:md5,789307aa335d21648043d8a9ffba6355"
             ],
             [
                 [
@@ -798,19 +798,19 @@
                 ],
                 [
                     "FAM_snv_annotated_ranked.vcf.gz",
-                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=2, variantCount=104, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=2, variantCount=114, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "FAM_snvs_annotated_ranked_filtered.vcf.gz",
-                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=55, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=65, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "HG002_Revio_A_snvs_annotated_ranked.vcf.gz",
-                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=100, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=113, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "HG002_Revio_B_snvs_annotated_ranked.vcf.gz",
-                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=100, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=112, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "FAM_svs_cnvs_merged_annotated_ranked.vcf.gz",
@@ -872,6 +872,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-16T14:56:19.363863667"
+        "timestamp": "2025-01-17T10:16:17.432290475"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/samplesheet_multisample_ont_bam.nf.test.snap b/tests/samplesheet_multisample_ont_bam.nf.test.snap
index 3a9c5c4e..abb9507e 100644
--- a/tests/samplesheet_multisample_ont_bam.nf.test.snap
+++ b/tests/samplesheet_multisample_ont_bam.nf.test.snap
@@ -64,10 +64,10 @@
                     "gawk": "5.1.0"
                 },
                 "DEEPVARIANT_RUNDEEPVARIANT": {
-                    "deepvariant": "1.6.1"
+                    "deepvariant": "1.8.0"
                 },
                 "DEEPVARIANT_VCFSTATSREPORT": {
-                    "deepvariant": "1.6.1"
+                    "deepvariant": "1.8.0"
                 },
                 "DIPCALL": {
                     "dipcall": 0.3
@@ -594,20 +594,20 @@
                 "HG002_ONT_B.hap2.sam.gz:md5,c6bbbc7fad9423840feb7b8cd18395b8",
                 "HG002_ONT_B.hap2.var.gz:md5,020812d4f3c94e5747855df872bf4ce8",
                 "HG002_ONT_B.pair.vcf.gz:md5,07cea4c96b9fe76b35952c46efcc6242",
-                "HG002_ONT_A_modkit_pileup_1.bed.gz:md5,2be86a42ac0384ac6d27fdf6e65304b7",
-                "HG002_ONT_A_modkit_pileup_1.bed.gz.tbi:md5,a7955eabc34456dce834a2c966071eaa",
-                "HG002_ONT_A_modkit_pileup_2.bed.gz:md5,ec565bd66fc73d380b7f9eb768369a65",
-                "HG002_ONT_A_modkit_pileup_2.bed.gz.tbi:md5,e6eb3c61b79a4abd0fd952f710d6eab3",
-                "HG002_ONT_A_modkit_pileup_ungrouped.bed.gz:md5,b42b812e1dced6242ed206754c7b3f3e",
-                "HG002_ONT_A_modkit_pileup_ungrouped.bed.gz.tbi:md5,0c232dffb9651d934b179f95365931db",
-                "HG002_ONT_B_modkit_pileup_1.bed.gz:md5,2be86a42ac0384ac6d27fdf6e65304b7",
-                "HG002_ONT_B_modkit_pileup_1.bed.gz.tbi:md5,a7955eabc34456dce834a2c966071eaa",
-                "HG002_ONT_B_modkit_pileup_2.bed.gz:md5,ec565bd66fc73d380b7f9eb768369a65",
-                "HG002_ONT_B_modkit_pileup_2.bed.gz.tbi:md5,e6eb3c61b79a4abd0fd952f710d6eab3",
-                "HG002_ONT_B_modkit_pileup_ungrouped.bed.gz:md5,42dcaedf8c379a4e5dee0822d5e8aca4",
-                "HG002_ONT_B_modkit_pileup_ungrouped.bed.gz.tbi:md5,3d97d016882c99e4e21112fc76ceb2a2",
-                "bcftools-stats-subtypes.txt:md5,1a8c8da19e5bc947cfb77de3683c8c00",
-                "bcftools_stats_indel-lengths.txt:md5,cc976b96114f0b68daffec58a7643d53",
+                "HG002_ONT_A_modkit_pileup_1.bed.gz:md5,a833ab3d48e7f94372edbefe8ca99e59",
+                "HG002_ONT_A_modkit_pileup_1.bed.gz.tbi:md5,a0c5a1faaf0373a58f97302b977e5595",
+                "HG002_ONT_A_modkit_pileup_2.bed.gz:md5,7c645581ccb6a55046d11f9a6f4b0d4a",
+                "HG002_ONT_A_modkit_pileup_2.bed.gz.tbi:md5,d4b3a3748199583bdcfabe40cd357d62",
+                "HG002_ONT_A_modkit_pileup_ungrouped.bed.gz:md5,7581d0c585c9b8d8457be41febaa285b",
+                "HG002_ONT_A_modkit_pileup_ungrouped.bed.gz.tbi:md5,aca974122b149ce92d210b2a0a8c1111",
+                "HG002_ONT_B_modkit_pileup_1.bed.gz:md5,a833ab3d48e7f94372edbefe8ca99e59",
+                "HG002_ONT_B_modkit_pileup_1.bed.gz.tbi:md5,a0c5a1faaf0373a58f97302b977e5595",
+                "HG002_ONT_B_modkit_pileup_2.bed.gz:md5,7c645581ccb6a55046d11f9a6f4b0d4a",
+                "HG002_ONT_B_modkit_pileup_2.bed.gz.tbi:md5,d4b3a3748199583bdcfabe40cd357d62",
+                "HG002_ONT_B_modkit_pileup_ungrouped.bed.gz:md5,6d5c696646cc1f74744f50cd51329970",
+                "HG002_ONT_B_modkit_pileup_ungrouped.bed.gz.tbi:md5,e8247ceb4f315285cb7bf3224afe9afe",
+                "bcftools-stats-subtypes.txt:md5,9640194a892bf60636bc15e93c320e5a",
+                "bcftools_stats_indel-lengths.txt:md5,02e19575017649b1402c865e6db8f164",
                 "fastqc-status-check-heatmap.txt:md5,03e5dc3abd2f2599a7bb03739dd5ca86",
                 "fastqc_adapter_content_plot.txt:md5,00c7bec7dd9304848f7d891d7d1fab7f",
                 "fastqc_overrepresented_sequences_plot.txt:md5,6f0148406e9d5358bf37375b33a4bc01",
@@ -625,14 +625,14 @@
                 "mosdepth_cov_dist.txt:md5,5ad1d589df3fa7fe5d21fc95001573a9",
                 "mosdepth_cumcov_dist.txt:md5,5ad1d589df3fa7fe5d21fc95001573a9",
                 "mosdepth_perchrom.txt:md5,86a907217d64d4c2717885403058580f",
-                "multiqc_bcftools_stats.txt:md5,41a78d00bdca33cf0d2a558bb60838db",
+                "multiqc_bcftools_stats.txt:md5,6737cc4c10024c7d475648fc197b330f",
                 "multiqc_citations.txt:md5,a27affce20d456d20ed387097a4f0350",
                 "multiqc_fastqc.txt:md5,ce26d17e62f3c8a1c9a01a871a4b9586",
-                "multiqc_general_stats.txt:md5,0814fb98fbb85e001e9c0c04d586d602",
-                "multiqc_whatshap_phased_bp_plot.txt:md5,e97b7038c7155326b5d6a2289cc0aeb7",
-                "multiqc_whatshap_stats.txt:md5,5c4b972c8d52b3d997f117b39ba3ad5d",
+                "multiqc_general_stats.txt:md5,1a87870cc6894a4d367dfaacc7f2317e",
+                "multiqc_whatshap_phased_bp_plot.txt:md5,2ab00ed124f9c20bf3e0c59e1b2d31aa",
+                "multiqc_whatshap_stats.txt:md5,eda3d216b4fb40afc041a401807f2747",
                 "somalier_stats.txt:md5,fec840d4fe202c0e3ff7ce94b2a3bf92",
-                "whatshap-stats-table.txt:md5,d552daaaef1c92c3351ec2f4de64e6ad",
+                "whatshap-stats-table.txt:md5,c4a84c623b8251228cb84d57e9984628",
                 "FAM.ped:md5,deb1ee6bd38d6e8f7cb92801d8a12f12",
                 "HG002_ONT_A_cramino_aligned_phased.arrow:md5,d2a5c81595fa34925ab8f03078487d81",
                 "HG002_ONT_B_cramino_aligned_phased.arrow:md5,61af72539e105cec79db7c9b78eb15a7",
@@ -648,16 +648,16 @@
                 "HG002_ONT_B.mosdepth.summary.txt:md5,bcb06b29c22cb6ad200f283e72c29653",
                 "HG002_ONT_B.regions.bed.gz:md5,1aa62d46a1e6683da3d44c59c502354b",
                 "HG002_ONT_B.regions.bed.gz.csi:md5,11db27a464f8996bae5521ee7d71c1ce",
-                "HG002_ONT_A_stats.blocks.tsv:md5,aac8023443ddf578ffcd11121391f1cf",
-                "HG002_ONT_A_stats.stats.tsv:md5,27fdac1e01e6491374c631239e6183aa",
-                "HG002_ONT_B_stats.blocks.tsv:md5,0adf84be03536262bf8d58eda524d709",
-                "HG002_ONT_B_stats.stats.tsv:md5,eb2a2c3b64feb8acff4df3a1b8d33b78",
+                "HG002_ONT_A_stats.blocks.tsv:md5,fda7110c817668520b340496f34a70f5",
+                "HG002_ONT_A_stats.stats.tsv:md5,f0d8f2ff4399fce2b6e665c7e5b59be8",
+                "HG002_ONT_B_stats.blocks.tsv:md5,ed60b095dba67127aaadf0e706421d99",
+                "HG002_ONT_B_stats.stats.tsv:md5,56313c39759bdd7c30c5b3c352e35fc5",
                 "HG002_ONT_A_hificnv.copynum.bedgraph:md5,4c5517c1783afa11ff93c8d8627fbe42",
                 "HG002_ONT_A_hificnv.depth.bw:md5,69c333b205994200641ea539b4c277c6",
-                "HG002_ONT_A_hificnv.maf.bw:md5,5b46c27cc53cc8dd68903738ab220c5f",
+                "HG002_ONT_A_hificnv.maf.bw:md5,460a692e4566462f69cf59dffcd94bc8",
                 "HG002_ONT_B_hificnv.copynum.bedgraph:md5,7d30f621d502d16301fa79cf48a3b903",
                 "HG002_ONT_B_hificnv.depth.bw:md5,5153fd5b008285e0fa0bcfe5026373bf",
-                "HG002_ONT_B_hificnv.maf.bw:md5,02eba7a84f1de8c042e071587a81d279"
+                "HG002_ONT_B_hificnv.maf.bw:md5,06b1ad43560eb183baeaedbe886320ca"
             ],
             [
                 [
@@ -720,27 +720,27 @@
                 ],
                 [
                     "HG002_ONT_A_phased.vcf.gz",
-                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=236, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=237, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "HG002_ONT_B_phased.vcf.gz",
-                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=236, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chrX, chr16, chr20], sampleCount=1, variantCount=237, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "FAM_snv_annotated_ranked.vcf.gz",
-                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=2, variantCount=105, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=2, variantCount=109, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "FAM_snvs_annotated_ranked_filtered.vcf.gz",
-                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=56, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chr16], sampleCount=2, variantCount=60, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "HG002_ONT_A_snvs_annotated_ranked.vcf.gz",
-                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=99, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=102, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "HG002_ONT_B_snvs_annotated_ranked.vcf.gz",
-                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=99, phased=false, phasedAutodetect=false]"
+                    "VcfFile [chromosomes=[chrX, chr16], sampleCount=1, variantCount=102, phased=false, phasedAutodetect=false]"
                 ],
                 [
                     "FAM_svs_cnvs_merged_annotated_ranked.vcf.gz",
@@ -790,6 +790,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2025-01-16T14:58:06.592348226"
+        "timestamp": "2025-01-17T10:18:21.407176156"
     }
-}
\ No newline at end of file
+}