diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8e347fc7c..92ced5cc9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1513](https://github.com/nf-core/sarek/pull/1513) - Back to dev
 - [#1518](https://github.com/nf-core/sarek/pull/1518) - Sync `TEMPLATE` with `tools` `2.14.1`
 - [#1521](https://github.com/nf-core/sarek/pull/1521) - Minor code refactoring to simplify syntax in args handling
+- [#1552](https://github.com/nf-core/sarek/pull/1552) - Update samtools to v1.20
 
 ### Fixed
 
@@ -31,6 +32,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Dependencies
 
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `samtools` | 1.19.2      | 1.20        |
+
 ### Modules / Subworkflows
 
 ### Parameters
diff --git a/conf/test.config b/conf/test.config
index 9dd0bca95..81567aed4 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -19,7 +19,7 @@ params {
     max_time   = '8.h'
 
     // Base directory for nf-core/modules test data
-    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules'
+    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
 
     // Input data
     input = "${projectDir}/tests/csv/3.0/fastq_single.csv"
diff --git a/modules.json b/modules.json
index dbcc04470..a4d96614b 100644
--- a/modules.json
+++ b/modules.json
@@ -356,47 +356,47 @@
                     },
                     "samtools/bam2fq": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/collatefastq": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/convert": {
                         "branch": "master",
-                        "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "f153f1f10e1083c49935565844cccb7453021682",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/mpileup": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "0bd7d2333a88483aa0476acea172e9f5f6dd83bb",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "sentieon/applyvarcal": {
diff --git a/modules/nf-core/samtools/bam2fq/environment.yml b/modules/nf-core/samtools/bam2fq/environment.yml
index 6f3c6d8b1..9c98946ad 100644
--- a/modules/nf-core/samtools/bam2fq/environment.yml
+++ b/modules/nf-core/samtools/bam2fq/environment.yml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.19.2
-  - bioconda::htslib=1.19.1
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf
index 463c6ae20..a34a13a98 100644
--- a/modules/nf-core/samtools/bam2fq/main.nf
+++ b/modules/nf-core/samtools/bam2fq/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_BAM2FQ {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
-        'biocontainers/samtools:1.19.2--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(inputbam)
diff --git a/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap b/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap
index 84da35bae..aa0f8c34d 100644
--- a/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap
@@ -51,25 +51,25 @@
     "bam_versions": {
         "content": [
             [
-                "versions.yml:md5,04115f386f1c3cb2e25edc02821da2fc"
+                "versions.yml:md5,90c1cf8971540ef05e330db5a560195c"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:13:56.124383258"
+        "timestamp": "2024-05-28T15:43:52.415053401"
     },
     "bam_split_versions": {
         "content": [
             [
-                "versions.yml:md5,04115f386f1c3cb2e25edc02821da2fc"
+                "versions.yml:md5,90c1cf8971540ef05e330db5a560195c"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:14:03.828077257"
+        "timestamp": "2024-05-28T15:43:57.740193087"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/samtools/collatefastq/environment.yml b/modules/nf-core/samtools/collatefastq/environment.yml
index d1ce1a801..93734c567 100644
--- a/modules/nf-core/samtools/collatefastq/environment.yml
+++ b/modules/nf-core/samtools/collatefastq/environment.yml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.19.2
-  - bioconda::htslib=1.19.1
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf
index 1e431c6e5..a75f56e8c 100644
--- a/modules/nf-core/samtools/collatefastq/main.nf
+++ b/modules/nf-core/samtools/collatefastq/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_COLLATEFASTQ {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
-        'biocontainers/samtools:1.19.2--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml
index cd4ee8c36..7a95ca614 100644
--- a/modules/nf-core/samtools/convert/environment.yml
+++ b/modules/nf-core/samtools/convert/environment.yml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.19.2
-  - bioconda::htslib=1.19.1
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf
index d61fbe2e3..03b7b5259 100644
--- a/modules/nf-core/samtools/convert/main.nf
+++ b/modules/nf-core/samtools/convert/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_CONVERT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
-        'biocontainers/samtools:1.19.2--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input), path(index)
diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test.snap b/modules/nf-core/samtools/convert/tests/main.nf.test.snap
index 3d6f88c4d..513629022 100644
--- a/modules/nf-core/samtools/convert/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/convert/tests/main.nf.test.snap
@@ -22,26 +22,26 @@
     "cram_to_bam_versions": {
         "content": [
             [
-                "versions.yml:md5,dd0aaf61f39c9ce91c74090f3c7ce1d0"
+                "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-06T11:14:51.308885706"
+        "timestamp": "2024-05-28T15:44:34.618037105"
     },
     "bam_to_cram_versions": {
         "content": [
             [
-                "versions.yml:md5,dd0aaf61f39c9ce91c74090f3c7ce1d0"
+                "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-06T11:14:36.643960504"
+        "timestamp": "2024-05-28T15:44:29.165839679"
     },
     "stub": {
         "content": [
@@ -71,7 +71,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,dd0aaf61f39c9ce91c74090f3c7ce1d0"
+                    "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd"
                 ],
                 "bai": [
                     
@@ -98,15 +98,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,dd0aaf61f39c9ce91c74090f3c7ce1d0"
+                    "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.03.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-03T12:01:40.896170698"
+        "timestamp": "2024-05-28T15:44:40.258233921"
     },
     "bam_to_cram_index": {
         "content": [
diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml
index 9c24eb0ab..f8450fa56 100644
--- a/modules/nf-core/samtools/faidx/environment.yml
+++ b/modules/nf-core/samtools/faidx/environment.yml
@@ -6,5 +6,5 @@ channels:
   - defaults
 
 dependencies:
-  - bioconda::htslib=1.19.1
-  - bioconda::samtools=1.19.2
+  - bioconda::htslib=1.20
+  - bioconda::samtools=1.20
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
index cfe7ad95f..bdcdbc954 100644
--- a/modules/nf-core/samtools/faidx/main.nf
+++ b/modules/nf-core/samtools/faidx/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
-        'biocontainers/samtools:1.19.2--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
index 3e651ef68..3223b72bc 100644
--- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap
@@ -18,7 +18,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
                 ],
                 "fa": [
                     
@@ -36,7 +36,7 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
                 ]
             }
         ],
@@ -44,7 +44,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-18T16:22:39.412601"
+        "timestamp": "2024-05-28T15:42:14.779784761"
     },
     "test_samtools_faidx_bgzip": {
         "content": [
@@ -71,7 +71,7 @@
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
                 ],
                 "fa": [
                     
@@ -95,7 +95,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
                 ]
             }
         ],
@@ -103,7 +103,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-18T16:23:22.427966"
+        "timestamp": "2024-05-28T15:42:20.256633877"
     },
     "test_samtools_faidx_fasta": {
         "content": [
@@ -124,7 +124,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
                 ],
                 "fa": [
                     [
@@ -142,7 +142,7 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
                 ]
             }
         ],
@@ -150,7 +150,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-18T16:24:04.107537"
+        "timestamp": "2024-05-28T15:42:25.632577273"
     },
     "test_samtools_faidx_stub_fasta": {
         "content": [
@@ -171,7 +171,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
                 ],
                 "fa": [
                     [
@@ -189,7 +189,7 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
                 ]
             }
         ],
@@ -197,7 +197,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-18T16:24:45.868463"
+        "timestamp": "2024-05-28T15:42:31.058424849"
     },
     "test_samtools_faidx_stub_fai": {
         "content": [
@@ -218,7 +218,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
                 ],
                 "fa": [
                     
@@ -236,7 +236,7 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,4870fc0a88c616aa937f8325a2db0c3c"
+                    "versions.yml:md5,2db78952923a61e05d50b95518b21856"
                 ]
             }
         ],
@@ -244,6 +244,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-03-18T16:25:27.550554"
+        "timestamp": "2024-05-28T15:42:36.479929617"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml
index a5e506498..260d516be 100644
--- a/modules/nf-core/samtools/index/environment.yml
+++ b/modules/nf-core/samtools/index/environment.yml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.19.2
-  - bioconda::htslib=1.19.1
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf
index dc14f98d6..b523c21b4 100644
--- a/modules/nf-core/samtools/index/main.nf
+++ b/modules/nf-core/samtools/index/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_INDEX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
-        'biocontainers/samtools:1.19.2--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap
index 3dc8e7de8..52756e85c 100644
--- a/modules/nf-core/samtools/index/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap
@@ -2,26 +2,26 @@
     "crai_versions": {
         "content": [
             [
-                "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e"
+                "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:12:00.324667957"
+        "timestamp": "2024-05-28T15:42:04.203740976"
     },
     "csi_versions": {
         "content": [
             [
-                "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e"
+                "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:12:07.885103162"
+        "timestamp": "2024-05-28T15:42:09.57475878"
     },
     "crai": {
         "content": [
@@ -62,13 +62,13 @@
     "bai_versions": {
         "content": [
             [
-                "versions.yml:md5,cc4370091670b64bba7c7206403ffb3e"
+                "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:11:51.641425452"
+        "timestamp": "2024-05-28T15:41:57.929287369"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml
index fc669b1b6..cd366d6de 100644
--- a/modules/nf-core/samtools/merge/environment.yml
+++ b/modules/nf-core/samtools/merge/environment.yml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.19.2
-  - bioconda::htslib=1.19.1
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf
index a3048c283..693b1d80f 100644
--- a/modules/nf-core/samtools/merge/main.nf
+++ b/modules/nf-core/samtools/merge/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_MERGE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
-        'biocontainers/samtools:1.19.2--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input_files, stageAs: "?/*")
diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap
index f7da7699b..17bc846fa 100644
--- a/modules/nf-core/samtools/merge/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/merge/tests/main.nf.test.snap
@@ -80,14 +80,14 @@
     "bam_versions": {
         "content": [
             [
-                "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4"
+                "versions.yml:md5,84dab54b9812780df48f5cecef690c34"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:16:33.782637377"
+        "timestamp": "2024-05-28T15:46:35.851936597"
     },
     "bams_csi": {
         "content": [
@@ -124,14 +124,14 @@
     "bams_stub_versions": {
         "content": [
             [
-                "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4"
+                "versions.yml:md5,84dab54b9812780df48f5cecef690c34"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:16:42.594476052"
+        "timestamp": "2024-05-28T15:46:41.405707643"
     },
     "bam_cram": {
         "content": [
@@ -158,14 +158,14 @@
     "bams_versions": {
         "content": [
             [
-                "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4"
+                "versions.yml:md5,84dab54b9812780df48f5cecef690c34"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:16:04.805335656"
+        "timestamp": "2024-05-28T15:45:51.695689923"
     },
     "crams_bam": {
         "content": [
@@ -182,14 +182,14 @@
     "crams_versions": {
         "content": [
             [
-                "versions.yml:md5,52c62d4712f7af00eb962d090ca32fe4"
+                "versions.yml:md5,84dab54b9812780df48f5cecef690c34"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:16:25.889394689"
+        "timestamp": "2024-05-28T15:46:30.185392319"
     },
     "bam_csi": {
         "content": [
diff --git a/modules/nf-core/samtools/mpileup/environment.yml b/modules/nf-core/samtools/mpileup/environment.yml
index 6628f5dc0..add717daf 100644
--- a/modules/nf-core/samtools/mpileup/environment.yml
+++ b/modules/nf-core/samtools/mpileup/environment.yml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.19.2
-  - bioconda::htslib=1.19.1
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf
index cb96181ff..b51f96d36 100644
--- a/modules/nf-core/samtools/mpileup/main.nf
+++ b/modules/nf-core/samtools/mpileup/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_MPILEUP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
-        'biocontainers/samtools:1.19.2--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
     input:
     tuple val(meta), path(input), path(intervals)
     path  fasta
diff --git a/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap b/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap
index fc891c1b7..76b2086b4 100644
--- a/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap
@@ -2,26 +2,26 @@
     "bam_bed_versions": {
         "content": [
             [
-                "versions.yml:md5,c617148132c6a529bdf506fd58ce6a9d"
+                "versions.yml:md5,449485eab74a465dc9023760be2c12a1"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:13:40.600861147"
+        "timestamp": "2024-05-28T15:43:41.535946155"
     },
     "bam_bed_fasta_versions": {
         "content": [
             [
-                "versions.yml:md5,c617148132c6a529bdf506fd58ce6a9d"
+                "versions.yml:md5,449485eab74a465dc9023760be2c12a1"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:13:48.271482127"
+        "timestamp": "2024-05-28T15:43:46.787790118"
     },
     "bam_bed_mpileup": {
         "content": [
diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml
index 67bb0ca40..1cc83bd95 100644
--- a/modules/nf-core/samtools/stats/environment.yml
+++ b/modules/nf-core/samtools/stats/environment.yml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.19.2
-  - bioconda::htslib=1.19.1
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf
index 52b00f4b6..982bc28e7 100644
--- a/modules/nf-core/samtools/stats/main.nf
+++ b/modules/nf-core/samtools/stats/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_STATS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
-        'biocontainers/samtools:1.19.2--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input), path(input_index)
diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap
index 1b7c9ba44..2747fd6c6 100644
--- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap
@@ -8,11 +8,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.stats:md5,01812900aa4027532906c5d431114233"
+                        "test.stats:md5,c9d39b38c22de2057fc2f89949090975"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9"
+                    "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a"
                 ],
                 "stats": [
                     [
@@ -20,19 +20,19 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.stats:md5,01812900aa4027532906c5d431114233"
+                        "test.stats:md5,c9d39b38c22de2057fc2f89949090975"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9"
+                    "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:15:25.562429714"
+        "timestamp": "2024-05-28T15:45:24.403941966"
     },
     "bam": {
         "content": [
@@ -43,11 +43,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.stats:md5,5d8681bf541199898c042bf400391d59"
+                        "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9"
+                    "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a"
                 ],
                 "stats": [
                     [
@@ -55,18 +55,18 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.stats:md5,5d8681bf541199898c042bf400391d59"
+                        "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0514ceb1769b2a88843e08c1f82624a9"
+                    "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:15:07.857611509"
+        "timestamp": "2024-05-28T15:45:06.711251947"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml
index b0676f338..150c37777 100644
--- a/modules/nf-core/samtools/view/environment.yml
+++ b/modules/nf-core/samtools/view/environment.yml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::samtools=1.19.2
-  - bioconda::htslib=1.19.1
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf
index 5a8989d69..38df85760 100644
--- a/modules/nf-core/samtools/view/main.nf
+++ b/modules/nf-core/samtools/view/main.nf
@@ -4,8 +4,8 @@ process SAMTOOLS_VIEW {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.19.2--h50ea8bc_0' :
-        'biocontainers/samtools:1.19.2--h50ea8bc_0' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
 
     input:
     tuple val(meta), path(input), path(index)
diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap
index f55943a7a..eb0c577c9 100644
--- a/modules/nf-core/samtools/view/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap
@@ -56,14 +56,14 @@
     "bam_stub_versions": {
         "content": [
             [
-                "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1"
+                "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:13:09.713353823"
+        "timestamp": "2024-05-28T15:43:20.390692583"
     },
     "cram_to_bam_index_cram": {
         "content": [
@@ -208,14 +208,14 @@
     "cram_to_bam_index_qname_versions": {
         "content": [
             [
-                "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1"
+                "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:13:03.935041046"
+        "timestamp": "2024-05-28T15:43:15.007493874"
     },
     "cram_to_bam_bam": {
         "content": [
@@ -240,14 +240,14 @@
     "cram_to_bam_index_versions": {
         "content": [
             [
-                "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1"
+                "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:12:55.910685496"
+        "timestamp": "2024-05-28T15:43:09.472376824"
     },
     "cram_to_bam_bai": {
         "content": [
@@ -264,14 +264,14 @@
     "cram_to_bam_versions": {
         "content": [
             [
-                "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1"
+                "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:12:47.715221169"
+        "timestamp": "2024-05-28T15:43:04.080050906"
     },
     "cram_bam": {
         "content": [
@@ -358,14 +358,14 @@
     "bam_versions": {
         "content": [
             [
-                "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1"
+                "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:12:31.692607421"
+        "timestamp": "2024-05-28T15:42:52.978954857"
     },
     "cram_to_bam_index_qname_cram": {
         "content": [
@@ -430,14 +430,14 @@
     "cram_versions": {
         "content": [
             [
-                "versions.yml:md5,4ea32c57d546102a1b32d9693ada7cf1"
+                "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-13T16:12:39.913411036"
+        "timestamp": "2024-05-28T15:42:58.400776109"
     },
     "bam_sam": {
         "content": [
diff --git a/tests/test_controlfreec.yml b/tests/test_controlfreec.yml
index d72b67ed2..5483c6946 100644
--- a/tests/test_controlfreec.yml
+++ b/tests/test_controlfreec.yml
@@ -19,11 +19,8 @@
           "window = 10",
         ]
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.bed
-      md5sum: 833920178e4f40a296d8eab029caf086
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.circos.txt
-      md5sum: 92ce5ce97b27a7214dfa9c2cb20cf854
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz_control.cpn
-      md5sum: 508a003da85b186d9a60d867ef7cdf15
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.p.value.txt
     # binary changes md5sums on reruns
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_BAF.txt
@@ -31,13 +28,10 @@
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_CNVs
     # binary changes md5sums on reruns
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_info.txt
-      md5sum: 271271719c576d9218bdc859850e54ee
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_ratio.BedGraph
-      md5sum: 5d3321af93678f16878d59e01d3a87d3
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_ratio.txt
     # binary changes md5sums on reruns
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_sample.cpn
-      md5sum: befe1706c61464635a76c7323a6bd2a2
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.png
     # binary changes md5sums on reruns
     - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.log2.png