diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml
index 20c91c6c128..1b636925f23 100644
--- a/.github/workflows/fix-linting.yml
+++ b/.github/workflows/fix-linting.yml
@@ -32,7 +32,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
+      - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 1bc54e1c92f..eb7144b5fd0 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -30,7 +30,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
       - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
         # FIXME Flip this off once we get to less than a couple hundred. Adding
         # this so it will only run against changed files. It'll make it much
@@ -45,7 +45,7 @@ jobs:
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
       - name: Install NodeJS
-        uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
+        uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4
         with:
           node-version: "20"
 
@@ -60,7 +60,7 @@ jobs:
     steps:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
-      - uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4
+      - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4
         with:
           node-version: "20"
 
@@ -151,7 +151,7 @@ jobs:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
       - name: Set up Python
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
         with:
           python-version: "3.11"
 
@@ -197,7 +197,7 @@ jobs:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
       - name: Set up Python
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
         with:
           python-version: "3.11"
 
@@ -413,7 +413,7 @@ jobs:
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
 
       - name: Set up Python
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
         with:
           python-version: "3.11"
 
@@ -664,7 +664,7 @@ jobs:
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
       - name: Set up Python
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5
         with:
           python-version: "3.11"
 
diff --git a/modules/nf-core/barrnap/main.nf b/modules/nf-core/barrnap/main.nf
index cd1143c9476..b99573d75f0 100644
--- a/modules/nf-core/barrnap/main.nf
+++ b/modules/nf-core/barrnap/main.nf
@@ -32,7 +32,7 @@ process BARRNAP {
         --threads $task.cpus \\
         --kingdom $db \\
         $input \\
-        > rrna_${db}.gff
+        > ${prefix}_${db}.gff
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -44,9 +44,9 @@ process BARRNAP {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
+    db = dbname ? "${dbname}" : 'bac'
     """
-    touch ${prefix}.gff
+    touch ${prefix}_${db}.gff
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/barrnap/meta.yml b/modules/nf-core/barrnap/meta.yml
index 3aaf407abb1..a683e712383 100644
--- a/modules/nf-core/barrnap/meta.yml
+++ b/modules/nf-core/barrnap/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: "https://github.com/tseemann/barrnap"
       documentation: "https://github.com/tseemann/barrnap"
       tool_dev_url: "https://github.com/tseemann/barrnap"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map
@@ -23,6 +23,9 @@ input:
       type: file
       description: fastq or fasta file nucleotides (it can be amino acids as well)
       pattern: "*.{fna,fasta,faa,fastq}"
+  - dbname:
+      type: string
+      description: database to use(bacteria, archaea, eukaryota, metazoan mitochondria)
 output:
   - meta:
       type: map
diff --git a/modules/nf-core/barrnap/tests/main.nf.test b/modules/nf-core/barrnap/tests/main.nf.test
new file mode 100644
index 00000000000..5e60932015d
--- /dev/null
+++ b/modules/nf-core/barrnap/tests/main.nf.test
@@ -0,0 +1,57 @@
+nextflow_process {
+
+    name "Test Process BARRNAP"
+    script "../main.nf"
+    process "BARRNAP"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "barrnap"
+
+    test("barrnap") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test', single_end:false ], // meta map
+                                file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+                                "bac"
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("barrnap - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test', single_end:false ], // meta map
+                                file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+                                "bac"
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
+
+
diff --git a/modules/nf-core/barrnap/tests/main.nf.test.snap b/modules/nf-core/barrnap/tests/main.nf.test.snap
new file mode 100644
index 00000000000..0964a0da270
--- /dev/null
+++ b/modules/nf-core/barrnap/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "barrnap - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_bac.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,447eafa60f76f6b84d1c41a2f5c2f76b"
+                ],
+                "gff": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_bac.gff:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,447eafa60f76f6b84d1c41a2f5c2f76b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-07-10T11:25:35.085998"
+    },
+    "barrnap": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_bac.gff:md5,df19e1b84ba6f691d20c72b397c88abf"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,447eafa60f76f6b84d1c41a2f5c2f76b"
+                ],
+                "gff": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_bac.gff:md5,df19e1b84ba6f691d20c72b397c88abf"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,447eafa60f76f6b84d1c41a2f5c2f76b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.1"
+        },
+        "timestamp": "2024-07-10T11:25:28.621027"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/barrnap/tests/tags.yml b/modules/nf-core/barrnap/tests/tags.yml
new file mode 100644
index 00000000000..5b951105515
--- /dev/null
+++ b/modules/nf-core/barrnap/tests/tags.yml
@@ -0,0 +1,2 @@
+barrnap:
+  - "modules/nf-core/barrnap/**"
diff --git a/modules/nf-core/bcftools/pluginsplit/main.nf b/modules/nf-core/bcftools/pluginsplit/main.nf
index 83de8f966d5..082802be709 100644
--- a/modules/nf-core/bcftools/pluginsplit/main.nf
+++ b/modules/nf-core/bcftools/pluginsplit/main.nf
@@ -15,8 +15,10 @@ process BCFTOOLS_PLUGINSPLIT {
     path(targets)
 
     output:
-    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}")  , emit: vcf
-    path "versions.yml"                                 , emit: versions
+    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
+    tuple val(meta), path("*.tbi")                    , emit: tbi, optional: true
+    tuple val(meta), path("*.csi")                    , emit: csi, optional: true
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,6 +34,7 @@ process BCFTOOLS_PLUGINSPLIT {
 
     """
     bcftools plugin split \\
+        ${args} \\
         ${vcf} \\
         ${samples_arg} \\
         ${groups_arg} \\
@@ -56,12 +59,17 @@ process BCFTOOLS_PLUGINSPLIT {
                 args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
                 args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
                 "vcf"
-
+    def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
+                args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
+                args.contains("--write-index") || args.contains("-W") ? "csi" :
+                ""
     def determination_file = samples ?: targets
+    def create_cmd = extension.matches("vcf|bcf") ? "touch " : "echo '' | gzip > "
+    def create_files = "cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt; while IFS= read -r filename; do ${create_cmd} \"\$filename\"; done < files.txt"
+    def create_index = index.matches("csi|tbi") ? "cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}.${index}/' > indices.txt; touch \$(<indices.txt)" : ""
     """
-    cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt
-
-    touch \$(<files.txt)
+    ${create_files}
+    ${create_index}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
new file mode 100644
index 00000000000..e3160851893
--- /dev/null
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
@@ -0,0 +1,192 @@
+nextflow_process {
+
+    name "Test Process BCFTOOLS_PLUGINSPLIT"
+    script "../main.nf"
+    process "BCFTOOLS_PLUGINSPLIT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "bcftools"
+    tag "bcftools/pluginsplit"
+
+    test("homo_sapiens - [ vcf, tbi ], samples, [], [], []") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
+                    .collectFile(name:"samples.txt", newLine:true)
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
+                    .collectFile(name:"samples.txt", newLine:true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.match).match() }
+
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi") {
+
+        config "./nextflow.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
+                    .collectFile(name:"samples.txt", newLine:true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.vcf,
+                    process.out.tbi.get(0).get(1).find { file(it).name.matches("normal.vcf.gz.tbi|tumor.vcf.gz.tbi") },
+                ) }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
+                    .collectFile(name:"samples.txt", newLine:true)
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
+                    .collectFile(name:"samples.txt", newLine:true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub") {
+
+        config "./nextflow.config"
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
+                    .collectFile(name:"samples.txt", newLine:true)
+                input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
new file mode 100644
index 00000000000..66c3c1dda5e
--- /dev/null
+++ b/modules/nf-core/bcftools/pluginsplit/tests/main.nf.test.snap
@@ -0,0 +1,240 @@
+{
+    "homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "tumour.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "tumour.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T15:56:42.307673651"
+    },
+    "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets": {
+        "content": null,
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T15:56:21.498991402"
+    },
+    "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "15000.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "40001.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "15000.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "40001.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "15000.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "40001.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "15000.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "40001.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T15:57:04.483688966"
+    },
+    "homo_sapiens - [ vcf, tbi ], samples, [], [], []": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf:md5,69cfc4bf92bf3e2847081a2026a4d3bb",
+                            "tumour.vcf:md5,08fa5c8d5561c2a8d7c300cb0eea1042"
+                        ]
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "normal.vcf:md5,69cfc4bf92bf3e2847081a2026a4d3bb",
+                            "tumour.vcf:md5,08fa5c8d5561c2a8d7c300cb0eea1042"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T15:56:10.033818589"
+    },
+    "homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "15000.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "40001.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "15000.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "40001.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8625f8c08503e47d029d48430c0bfccc"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T15:56:53.641165787"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/nextflow.config b/modules/nf-core/bcftools/pluginsplit/tests/nextflow.config
new file mode 100644
index 00000000000..9b9a4783a57
--- /dev/null
+++ b/modules/nf-core/bcftools/pluginsplit/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'BCFTOOLS_PLUGINSPLIT' {
+        ext.args = '--write-index=tbi --output-type z'
+    }
+}
diff --git a/modules/nf-core/bcftools/pluginsplit/tests/tags.yml b/modules/nf-core/bcftools/pluginsplit/tests/tags.yml
new file mode 100644
index 00000000000..2f29ef18ac8
--- /dev/null
+++ b/modules/nf-core/bcftools/pluginsplit/tests/tags.yml
@@ -0,0 +1,2 @@
+bcftools/pluginsplit:
+  - "modules/nf-core/bcftools/pluginsplit/**"
diff --git a/modules/nf-core/bclconvert/Dockerfile b/modules/nf-core/bclconvert/Dockerfile
index 2124c7942dc..a165493c85b 100644
--- a/modules/nf-core/bclconvert/Dockerfile
+++ b/modules/nf-core/bclconvert/Dockerfile
@@ -3,7 +3,7 @@
 # Push to nfcore/bclconvert:<VER>
 
 FROM debian:bullseye-slim
-ARG BCLCONVERT_VERSION="4.2.7"
+ARG BCLCONVERT_VERSION="4.3.6"
 LABEL org.opencontainers.image.authors="Matthias De Smet <matthias.desmet@ugent.be>"
 LABEL org.opencontainers.image.description="Docker image containing bcl-convert"
 LABEL org.opencontainers.image.version="$BCLCONVERT_VERSION"
@@ -25,9 +25,7 @@ RUN apt-get update \
 # Link hostname cmd to fix hardcoded path
 RUN ln -s /bin/hostname /usr/bin/hostname
 # Install bcl-convert
-ADD --checksum=sha256:ea508d763dc27d30d1a34f6a38d8da31ea67797d7b4971e8c10677bc48539565 \
-    https://s3.amazonaws.com/webdata.illumina.com/downloads/software/bcl-convert/bcl-convert-${BCLCONVERT_VERSION}-2.el7.x86_64.rpm \
-    bcl-convert.rpm
+ADD bcl-convert-4.3.6-2.el8.x86_64.rpm bcl-convert.rpm
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 RUN rpm2cpio bcl-convert.rpm | cpio -idmv \
     && rm bcl-convert.rpm
diff --git a/modules/nf-core/bclconvert/README.md b/modules/nf-core/bclconvert/README.md
index 54679d0f33a..63197d166eb 100644
--- a/modules/nf-core/bclconvert/README.md
+++ b/modules/nf-core/bclconvert/README.md
@@ -2,8 +2,8 @@
 
 bcl-convert is a commercial tool from Illumina. The container provided for the bcl-convert nf-core module is not provided nor supported by Illumina. Updating the bcl-convert versions in the container and pushing the update to Dockerhub needs to be done manually.
 
-1. Navigate to the appropriate download page. - [BCL Convert](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/downloads.html): find the latest version of bcl-convert
-2. Update the `BCL_VERSION` in the `Dockerfile` (You might have to update the link in the `ADD` statement)
+1. Navigate to the appropriate download page. - [BCL Convert](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/downloads.html): find and download the latest version of bcl-convert RPM package.
+2. Update the `BCL_VERSION` in the `Dockerfile`
 3. Create and test the container:
 
    ```bash
diff --git a/modules/nf-core/bclconvert/main.nf b/modules/nf-core/bclconvert/main.nf
index 8e6886dfc6f..553bd318d32 100644
--- a/modules/nf-core/bclconvert/main.nf
+++ b/modules/nf-core/bclconvert/main.nf
@@ -2,7 +2,7 @@ process BCLCONVERT {
     tag {"$meta.lane" ? "$meta.id"+"."+"$meta.lane" : "$meta.id" }
     label 'process_high'
 
-    container "nf-core/bclconvert:4.2.7"
+    container "nf-core/bclconvert:4.3.6"
 
     input:
     tuple val(meta), path(samplesheet), path(run_dir)
diff --git a/modules/nf-core/bclconvert/tests/main.nf.test.snap b/modules/nf-core/bclconvert/tests/main.nf.test.snap
index 8b9d506c450..aa6eae8a61c 100644
--- a/modules/nf-core/bclconvert/tests/main.nf.test.snap
+++ b/modules/nf-core/bclconvert/tests/main.nf.test.snap
@@ -24,7 +24,7 @@
                 ]
             ],
             [
-                "versions.yml:md5,375aa95eef22ad3b0cc39b325d7ac9e0"
+                "versions.yml:md5,3742a25082bc9f0ff8dca303c5c8cb8b"
             ],
             [
                 [
@@ -50,6 +50,10 @@
                 "TileMetricsOut.bin:md5,83891751ec1c91a425a524b476b6ca3c"
             ]
         ],
-        "timestamp": "2024-01-31T13:06:35.609496414"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T11:36:50.00930061"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/dupradar/templates/dupradar.r b/modules/nf-core/dupradar/templates/dupradar.r
index ec20cb85147..7653e587397 100755
--- a/modules/nf-core/dupradar/templates/dupradar.r
+++ b/modules/nf-core/dupradar/templates/dupradar.r
@@ -88,7 +88,6 @@ line="#id: DupInt
 #        max: 100
 #        min: 0
 #        scale: 'RdYlGn-rev'
-#        format: '{:.2f}%'
 Sample dupRadar_intercept"
 
 write(line,file=paste0(output_prefix, "_dup_intercept_mqc.txt"),append=TRUE)
@@ -115,29 +114,23 @@ line="#id: dupradar
 #    This plot shows the general linear models - a summary of the gene duplication distributions. \"
 #pconfig:
 #    title: 'DupRadar General Linear Model'
-#    xLog: True
+#    xlog: True
 #    xlab: 'expression (reads/kbp)'
 #    ylab: '% duplicate reads'
 #    ymax: 100
 #    ymin: 0
 #    tt_label: '<b>{point.x:.1f} reads/kbp</b>: {point.y:,.2f}% duplicates'
-#    xPlotLines:
+#    x_lines:
 #        - color: 'green'
-#          dashStyle: 'LongDash'
+#          dash: 'LongDash'
 #          label:
-#                style: {color: 'green'}
 #                text: '0.5 RPKM'
-#                verticalAlign: 'bottom'
-#                y: -65
 #          value: 0.5
 #          width: 1
 #        - color: 'red'
-#          dashStyle: 'LongDash'
+#          dash: 'LongDash'
 #          label:
-#                style: {color: 'red'}
 #                text: '1 read/bp'
-#                verticalAlign: 'bottom'
-#                y: -65
 #          value: 1000
 #          width: 1"
 
diff --git a/modules/nf-core/dupradar/tests/main.nf.test.snap b/modules/nf-core/dupradar/tests/main.nf.test.snap
index 0b38d4be180..dc7aba4a55a 100644
--- a/modules/nf-core/dupradar/tests/main.nf.test.snap
+++ b/modules/nf-core/dupradar/tests/main.nf.test.snap
@@ -23,8 +23,8 @@
                         "strandedness": "forward"
                     },
                     [
-                        "test_dup_intercept_mqc.txt:md5,7b6fb70cbede0d20ffa576a0cc0b249d",
-                        "test_duprateExpDensCurve_mqc.txt:md5,49b44937123c14b622f346cb6156dd4f"
+                        "test_dup_intercept_mqc.txt:md5,11961f0962ffc70e42aa57a12984e0fc",
+                        "test_duprateExpDensCurve_mqc.txt:md5,f7d3432ef52047336b156446281aa6ac"
                     ]
                 ]
             ],
@@ -36,7 +36,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-05T13:26:49.615507"
+        "timestamp": "2024-07-11T11:21:44.31238184"
     },
     "sarscov2 - bam - single_end - stub": {
         "content": [
@@ -199,7 +199,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-05T13:27:00.623697"
+        "timestamp": "2024-07-11T11:21:56.741878886"
     },
     "sarscov2 - bam - paired_end": {
         "content": [
@@ -225,8 +225,8 @@
                         "strandedness": "forward"
                     },
                     [
-                        "test_dup_intercept_mqc.txt:md5,d69369924aeb9695b0e97e755e0d9ea3",
-                        "test_duprateExpDensCurve_mqc.txt:md5,f4a50dc09de81219ed4449c11153ba6e"
+                        "test_dup_intercept_mqc.txt:md5,002855b42a71aa0f407ef7fa19df9ac3",
+                        "test_duprateExpDensCurve_mqc.txt:md5,e797d8e256c5b2ab3aad1801360f1a77"
                     ]
                 ]
             ],
@@ -238,7 +238,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-05T13:27:11.791811"
+        "timestamp": "2024-07-11T11:22:10.053957095"
     },
     "sarscov2 - bam - paired_end - stub": {
         "content": [
@@ -401,6 +401,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-05T13:27:22.967266"
+        "timestamp": "2024-07-11T11:22:22.134058061"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/glimpse2/phase/main.nf b/modules/nf-core/glimpse2/phase/main.nf
index d61bd9b8826..5419f95beb9 100644
--- a/modules/nf-core/glimpse2/phase/main.nf
+++ b/modules/nf-core/glimpse2/phase/main.nf
@@ -18,11 +18,11 @@ process GLIMPSE2_PHASE {
         'biocontainers/glimpse-bio:2.0.1--h46b9e50_1' }"
 
     input:
-        tuple val(meta) , path(input), path(input_index), path(samples_file), val(input_region), val(output_region), path(reference), path(reference_index), path(map)
+        tuple val(meta) , path(input, arity: '1..*'), path(input_index), path(samples_file), val(input_region), val(output_region), path(reference), path(reference_index), path(map)
         tuple val(meta2), path(fasta_reference), path(fasta_reference_index)
 
     output:
-        tuple val(meta), path("*.{vcf,bcf,bgen}"), emit: phased_variants
+        tuple val(meta), path("*.{vcf,vcf.gz,bcf,bgen}"), emit: phased_variants
         tuple val(meta), path("*.txt.gz")        , emit: stats_coverage, optional: true
         path "versions.yml"                      , emit: versions
 
@@ -41,15 +41,39 @@ process GLIMPSE2_PHASE {
     def input_region_cmd      = input_region        ? "--input-region $input_region"  : ""
     def output_region_cmd     = output_region       ? "--output-region $output_region": ""
 
-    def input_bam             = input.any { it.extension in ["cram","bam"]}
+    def input_type            = input.collect{
+        it.toString().endsWithAny("cram", "bam") ? "bam" :
+        it.toString().endsWithAny("vcf", "bcf", "vcf.gz") ? "gl" :
+        it.getExtension()
+        }.unique()
+
+    if (input_type.size() > 1 | !(input_type.contains("gl") | input_type.contains("bam"))) {
+        error "Input files must be of the same type and either .bam/.cram or .vcf/.vcf.gz/.bcf format. Found: ${input_type}"
+    } else {
+        input_type = input_type[0]
+    }
+    if (input_type == "gl" & input.size() > 1) {
+        error "Only one input .vcf/.vcf.gz/.bcf file can be provided"
+    }
+    def input_list = input.size() > 1
 
     """
-    if $input_bam
+    if $input_list ;
     then
         ls -1 | grep '\\.cram\$\\|\\.bam\$' > all_bam.txt
         input_command="--bam-list all_bam.txt"
     else
-        input_command="--input-gl $input"
+        if [ "$input_type" == "bam" ];
+        then
+            input_command="--bam-file $input"
+        elif [ "$input_type" == "gl" ];
+        then
+            input_command="--input-gl $input"
+        else
+            echo "Input file type not recognised"
+            echo "$input_type"
+            exit 1
+        fi
     fi
 
     GLIMPSE2_phase \\
diff --git a/modules/nf-core/glimpse2/phase/meta.yml b/modules/nf-core/glimpse2/phase/meta.yml
index db2595e6b3f..700b6204fe5 100644
--- a/modules/nf-core/glimpse2/phase/meta.yml
+++ b/modules/nf-core/glimpse2/phase/meta.yml
@@ -22,7 +22,7 @@ input:
   - input:
       type: file
       description: |
-        Either multiple BAM/CRAM files containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods.
+        Either one or multiple BAM/CRAM files in an array containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods.
         When using BAM/CRAM the name of the file is used as samples name.
       pattern: "*.{bam,cram,vcf,vcf.gz,bcf,bcf.gz}"
   - input_index:
diff --git a/modules/nf-core/glimpse2/phase/tests/main.nf.test b/modules/nf-core/glimpse2/phase/tests/main.nf.test
index 95c6d9e1c69..69642590a4e 100644
--- a/modules/nf-core/glimpse2/phase/tests/main.nf.test
+++ b/modules/nf-core/glimpse2/phase/tests/main.nf.test
@@ -141,4 +141,140 @@ nextflow_process {
             )
         }
     }
+    test("Should run with list of bam files and reference genome") {
+
+        when {
+            process {
+                """
+                input_bam = Channel.of([
+                    [id:'input'],
+                    [file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.bam", checkIfExists: true),
+                     file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA19401/NA19401.s.bam", checkIfExists: true)],
+                    [file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.bam.bai", checkIfExists: true),
+                     file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA19401/NA19401.s.bam.bai", checkIfExists: true)],
+                    [],
+                    "chr21:16600000-16800000",
+                    "chr21:16650000-16750000",
+                ])
+                ref_panel = Channel.of([
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
+                ])
+
+                map_file = Channel.of([
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true)
+                ])
+                reference_genome = Channel.of([
+                    [id:'refHG38_chr21'],
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/hs38DH.chr21.fa.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/hs38DH.chr21.fa.gz.fai", checkIfExists: true)
+                    ])
+                // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
+                input[0] = input_bam
+                    .combine(ref_panel)
+                    .combine(map_file)
+                input[1] = reference_genome
+                """
+                }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                // File has a timestamp in it and is in binary format, so we can only check the name
+                { assert file(process.out.phased_variants[0][1]).name == "input_chr21_16650000-16750000.bcf" },
+                { assert snapshot(process.out.stats_coverage).match("List_coverage")},
+                { assert snapshot(process.out.versions).match("List_versions")}
+            )
+        }
+    }
+
+    test("Should run into error file type inconsistent") {
+
+        when {
+            process {
+                """
+                input_bam = Channel.of([
+                    [id:'input'],
+                    [file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.bam", checkIfExists: true),
+                     file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true)],
+                    [file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.bam.bai", checkIfExists: true),
+                     file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)],
+                    [],
+                    "chr21:16600000-16800000",
+                    "chr21:16650000-16750000",
+                ])
+                ref_panel = Channel.of([
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
+                ])
+
+                map_file = Channel.of([
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true)
+                ])
+                reference_genome = Channel.of([
+                    [id:'refHG38_chr21'],
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/hs38DH.chr21.fa.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/hs38DH.chr21.fa.gz.fai", checkIfExists: true)
+                    ])
+                // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
+                input[0] = input_bam
+                    .combine(ref_panel)
+                    .combine(map_file)
+                input[1] = reference_genome
+                """
+                }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed },
+                { assert process.errorReport.contains("Input files must be of the same type and either .bam/.cram or .vcf/.vcf.gz/.bcf format. Found: [bam, gl]") }
+            )
+        }
+    }
+
+    test("Should run into error only one vcf allowed") {
+        when {
+            process {
+                """
+                input_bam = Channel.of([
+                    [id:'input'],
+                    [file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bcf", checkIfExists: true),
+                     file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true)],
+                    [file("https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/data/individuals/NA12878/NA12878.s.1x.bcf.csi", checkIfExists: true),
+                     file(params.modules_testdata_base_path + "delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true)],
+                    [],
+                    "chr21:16600000-16800000",
+                    "chr21:16650000-16750000",
+                ])
+                ref_panel = Channel.of([
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
+                ])
+
+                map_file = Channel.of([
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true)
+                ])
+                reference_genome = Channel.of([
+                    [id:'refHG38_chr21'],
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/hs38DH.chr21.fa.gz", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "delete_me/glimpse/hs38DH.chr21.fa.gz.fai", checkIfExists: true)
+                    ])
+                // [meta, vcf, index, sample_infos, regionin, regionout,ref, index, map] [meta, fasta, fai]
+                input[0] = input_bam
+                    .combine(ref_panel)
+                    .combine(map_file)
+                input[1] = reference_genome
+                """
+                }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed },
+                { assert process.errorReport.contains("Only one input .vcf/.vcf.gz/.bcf file can be provided") }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/glimpse2/phase/tests/main.nf.test.snap b/modules/nf-core/glimpse2/phase/tests/main.nf.test.snap
index 861f9a70eb6..d32e27c3aea 100644
--- a/modules/nf-core/glimpse2/phase/tests/main.nf.test.snap
+++ b/modules/nf-core/glimpse2/phase/tests/main.nf.test.snap
@@ -23,6 +23,35 @@
         },
         "timestamp": "2024-03-13T16:58:05.013609832"
     },
+    "List_coverage": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "input"
+                    },
+                    "input_chr21_16650000-16750000_stats_coverage.txt.gz:md5,ac61370fc14738b103e160b7298727b9"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-07-09T20:35:30.943277837"
+    },
+    "List_versions": {
+        "content": [
+            [
+                "versions.yml:md5,c68de03046a6503cdbcf3a1495fc512f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-07-09T20:35:30.97466287"
+    },
     "BAM_coverage": {
         "content": [
             [
diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf
index edf92a38461..560ada11b32 100644
--- a/modules/nf-core/last/lastal/main.nf
+++ b/modules/nf-core/last/lastal/main.nf
@@ -13,6 +13,7 @@ process LAST_LASTAL {
 
     output:
     tuple val(meta), path("*.maf.gz"), emit: maf
+    tuple val(meta), path("*.tsv")   , emit: multiqc
     path "versions.yml"              , emit: versions
 
     when:
@@ -25,15 +26,33 @@ process LAST_LASTAL {
     """
     INDEX_NAME=\$(basename \$(ls $index/*.des) .des)
     set -o pipefail
+
+    function calculate_psl_metrics() {
+        awk 'BEGIN {
+            FS="\t";  # Set field separator as tab
+            totalMatches = 0;
+            totalAlignmentLength = 0;
+            print "Sample\tTotalAlignmentLength\tPercentSimilarity";  # Header for MultiQC
+        }
+        {
+            totalMatches += \$1 + \$3;  # Sum matches and repMatches
+            totalAlignmentLength += \$1 + \$2 + \$3 + \$6 + \$8;  # Sum matches, misMatches, repMatches, qBaseInsert, and tBaseInsert
+        }
+        END {
+            percentSimilarity = (totalAlignmentLength > 0) ? (totalMatches / totalAlignmentLength * 100) : 0;
+            print "$meta.id" "\t" totalAlignmentLength "\t" percentSimilarity;  # Data in TSV format
+        }'
+    }
+
     lastal \\
         -P $task.cpus \\
         $trained_params \\
         $args \\
         ${index}/\$INDEX_NAME \\
-        $fastx \\
-        | gzip --no-name > ${prefix}.\$INDEX_NAME.maf.gz
-    # gzip needs --no-name otherwise it puts a timestamp in the file,
-    # which makes its checksum non-reproducible.
+        $fastx |
+        tee >(gzip --no-name  > ${prefix}.maf.gz) |
+        maf-convert psl |
+        calculate_psl_metrics > ${prefix}.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -48,6 +67,7 @@ process LAST_LASTAL {
     """
     INDEX_NAME=STUB
     echo stub | gzip --no-name > ${prefix}.\$INDEX_NAME.maf.gz
+    touch ${prefix}.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/last/lastal/meta.yml b/modules/nf-core/last/lastal/meta.yml
index 7e416f7f342..c14fa27989d 100644
--- a/modules/nf-core/last/lastal/meta.yml
+++ b/modules/nf-core/last/lastal/meta.yml
@@ -46,6 +46,10 @@ output:
       type: file
       description: Gzipped MAF (Multiple Alignment Format) file
       pattern: "*.{maf.gz}"
+  - multiqc:
+      type: file
+      description: Alignment summary for MultiQC
+      pattern: "*.tsv"
 authors:
   - "@charles-plessy"
 maintainers:
diff --git a/modules/nf-core/last/lastal/tests/main.nf.test.snap b/modules/nf-core/last/lastal/tests/main.nf.test.snap
index ba054b089a8..9245a96252e 100644
--- a/modules/nf-core/last/lastal/tests/main.nf.test.snap
+++ b/modules/nf-core/last/lastal/tests/main.nf.test.snap
@@ -8,10 +8,19 @@
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.genome.maf.gz:md5,902274b72657f62d270d284dc211aa7f"
+                        "contigs.maf.gz:md5,902274b72657f62d270d284dc211aa7f"
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "contigs",
+                            "single_end": false
+                        },
+                        "contigs.tsv:md5,f028e69bd64e54080b9a03fd809cba74"
+                    ]
+                ],
+                "2": [
                     "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2"
                 ],
                 "maf": [
@@ -20,7 +29,16 @@
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.genome.maf.gz:md5,902274b72657f62d270d284dc211aa7f"
+                        "contigs.maf.gz:md5,902274b72657f62d270d284dc211aa7f"
+                    ]
+                ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "contigs",
+                            "single_end": false
+                        },
+                        "contigs.tsv:md5,f028e69bd64e54080b9a03fd809cba74"
                     ]
                 ],
                 "versions": [
@@ -32,7 +50,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-06T23:11:59.764152"
+        "timestamp": "2024-07-02T17:57:48.589408"
     },
     "sarscov2 - contigs - genome - stub": {
         "content": [
@@ -47,6 +65,15 @@
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "contigs",
+                            "single_end": false
+                        },
+                        "contigs.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
                     "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2"
                 ],
                 "maf": [
@@ -58,6 +85,15 @@
                         "contigs.STUB.maf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260"
                     ]
                 ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "contigs",
+                            "single_end": false
+                        },
+                        "contigs.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "versions": [
                     "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2"
                 ]
@@ -67,7 +103,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-06T23:12:43.028075"
+        "timestamp": "2024-07-02T17:58:30.521811"
     },
     "sarscov2 - contigs - genome - withparams": {
         "content": [
@@ -78,10 +114,19 @@
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.genome.maf.gz:md5,8cb97b6daa34dbf9c723a2c4a984992d"
+                        "contigs.maf.gz:md5,8cb97b6daa34dbf9c723a2c4a984992d"
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "contigs",
+                            "single_end": false
+                        },
+                        "contigs.tsv:md5,f315664aa18f1f6bad79486f9750f200"
+                    ]
+                ],
+                "2": [
                     "versions.yml:md5,e0a425d7cbca674252a1e4328b247ca2"
                 ],
                 "maf": [
@@ -90,7 +135,16 @@
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.genome.maf.gz:md5,8cb97b6daa34dbf9c723a2c4a984992d"
+                        "contigs.maf.gz:md5,8cb97b6daa34dbf9c723a2c4a984992d"
+                    ]
+                ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "contigs",
+                            "single_end": false
+                        },
+                        "contigs.tsv:md5,f315664aa18f1f6bad79486f9750f200"
                     ]
                 ],
                 "versions": [
@@ -102,6 +156,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-06T23:12:21.536568"
+        "timestamp": "2024-07-02T17:58:09.677672"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf
index 4b29d912fb4..410d16f1d27 100644
--- a/modules/nf-core/last/split/main.nf
+++ b/modules/nf-core/last/split/main.nf
@@ -12,6 +12,7 @@ process LAST_SPLIT {
 
     output:
     tuple val(meta), path("*.maf.gz"), emit: maf
+    tuple val(meta), path("*.tsv")   , emit: multiqc
     path "versions.yml"              , emit: versions
 
     when:
@@ -23,7 +24,29 @@ process LAST_SPLIT {
     if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     set -o pipefail
-    zcat < $maf | last-split $args | gzip --no-name > ${prefix}.maf.gz
+
+    function calculate_psl_metrics() {
+        awk 'BEGIN {
+            FS="\t";  # Set field separator as tab
+            totalMatches = 0;
+            totalAlignmentLength = 0;
+            print "Sample\tTotalAlignmentLength\tPercentSimilarity";  # Header for MultiQC
+        }
+        {
+            totalMatches += \$1 + \$3;  # Sum matches and repMatches
+            totalAlignmentLength += \$1 + \$2 + \$3 + \$6 + \$8;  # Sum matches, misMatches, repMatches, qBaseInsert, and tBaseInsert
+        }
+        END {
+            percentSimilarity = (totalAlignmentLength > 0) ? (totalMatches / totalAlignmentLength * 100) : 0;
+            print "$meta.id" "\t" totalAlignmentLength "\t" percentSimilarity;  # Data in TSV format
+        }'
+    }
+
+    zcat < $maf |
+        last-split $args |
+        tee >(gzip --no-name  > ${prefix}.maf.gz) |
+        maf-convert psl |
+        calculate_psl_metrics > ${prefix}.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -37,6 +60,7 @@ process LAST_SPLIT {
     if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     echo stub | gzip --no-name > ${prefix}.maf.gz
+    touch ${prefix}.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/last/split/meta.yml b/modules/nf-core/last/split/meta.yml
index 03b030f9bbe..2e23f8b4c6a 100644
--- a/modules/nf-core/last/split/meta.yml
+++ b/modules/nf-core/last/split/meta.yml
@@ -40,6 +40,10 @@ output:
       type: file
       description: Multiple Aligment Format (MAF) file, compressed with gzip
       pattern: "*.{maf.gz}"
+  - multiqc:
+      type: file
+      description: Alignment summary for MultiQC
+      pattern: "*.tsv"
 authors:
   - "@aleksandrabliznina"
   - "@charles-plessy"
diff --git a/modules/nf-core/last/split/tests/main.nf.test.snap b/modules/nf-core/last/split/tests/main.nf.test.snap
index 85a9c087a03..953a6542a80 100644
--- a/modules/nf-core/last/split/tests/main.nf.test.snap
+++ b/modules/nf-core/last/split/tests/main.nf.test.snap
@@ -11,6 +11,14 @@
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "sarscov.contigs.genome"
+                        },
+                        "sarscov.contigs.genome.tsv:md5,b625a3b37343e9e6a279b8625d4c2da8"
+                    ]
+                ],
+                "2": [
                     "versions.yml:md5,9e429d0800988ae0bbe5000827d34ad1"
                 ],
                 "maf": [
@@ -21,6 +29,14 @@
                         "sarscov.contigs.genome.maf.gz:md5,689cb18ff7098ff90eaf87017f590208"
                     ]
                 ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "sarscov.contigs.genome"
+                        },
+                        "sarscov.contigs.genome.tsv:md5,b625a3b37343e9e6a279b8625d4c2da8"
+                    ]
+                ],
                 "versions": [
                     "versions.yml:md5,9e429d0800988ae0bbe5000827d34ad1"
                 ]
@@ -30,7 +46,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-06T17:49:24.045661"
+        "timestamp": "2024-07-02T11:45:00.535348"
     },
     "sarscov2 - contigs_genome - stub": {
         "content": [
@@ -44,6 +60,14 @@
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "sarscov.contigs.genome"
+                        },
+                        "sarscov.contigs.genome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
                     "versions.yml:md5,9e429d0800988ae0bbe5000827d34ad1"
                 ],
                 "maf": [
@@ -54,6 +78,14 @@
                         "sarscov.contigs.genome.maf.gz:md5,f50b84b1db4b83ba62ec1deacc69c260"
                     ]
                 ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "sarscov.contigs.genome"
+                        },
+                        "sarscov.contigs.genome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "versions": [
                     "versions.yml:md5,9e429d0800988ae0bbe5000827d34ad1"
                 ]
@@ -63,6 +95,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-06T17:50:20.139442"
+        "timestamp": "2024-07-02T11:45:21.243325"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf
index 67938716beb..10bed777300 100644
--- a/modules/nf-core/last/train/main.nf
+++ b/modules/nf-core/last/train/main.nf
@@ -13,6 +13,7 @@ process LAST_TRAIN {
 
     output:
     tuple val(meta), path("*.train"), emit: param_file
+    tuple val(meta), path("*.tsv")  , emit: multiqc
     path "versions.yml"           , emit: versions
 
     when:
@@ -31,6 +32,16 @@ process LAST_TRAIN {
         $fastx \\
         > ${prefix}.\$INDEX_NAME.train
 
+    echo "id\tsubstitution_percent_identity\tlast -t\tlast -a\tlast -A\tlast -b\tlast -B\tlast -S" > ${prefix}.train.tsv
+    printf "\$(basename ${prefix}.\$INDEX_NAME.train .target.train)\t" >> ${prefix}.train.tsv
+    grep 'substitution percent identity' ${prefix}.\$INDEX_NAME.train | tail -n 1 | awk '{print \$5}' | tr '\n' '\t' >> ${prefix}.train.tsv
+    grep 'last -t' ${prefix}.\$INDEX_NAME.train | tail -n 1 | awk '{print \$2}' | sed -e 's/-t//' | tr '\n' '\t' >> ${prefix}.train.tsv
+    grep 'last -a' ${prefix}.\$INDEX_NAME.train | tail -n 1 | awk '{print \$3}' | tr '\n' '\t' >> ${prefix}.train.tsv
+    grep 'last -A' ${prefix}.\$INDEX_NAME.train | tail -n 1 | awk '{print \$3}' | tr '\n' '\t' >> ${prefix}.train.tsv
+    grep 'last -b' ${prefix}.\$INDEX_NAME.train | tail -n 1 | awk '{print \$3}' | tr '\n' '\t' >> ${prefix}.train.tsv
+    grep 'last -B' ${prefix}.\$INDEX_NAME.train | tail -n 1 | awk '{print \$3}' | tr '\n' '\t' >> ${prefix}.train.tsv
+    grep 'last -S' ${prefix}.\$INDEX_NAME.train | tail -n 1 | awk '{print \$3}' >> ${prefix}.train.tsv
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         last: \$(lastdb --version | sed 's/lastdb //')
@@ -43,6 +54,7 @@ process LAST_TRAIN {
     """
     INDEX_NAME=STUB
     touch ${prefix}.\$INDEX_NAME.train
+    touch ${prefix}.train.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/last/train/meta.yml b/modules/nf-core/last/train/meta.yml
index db723be5ba9..d55e82734b3 100644
--- a/modules/nf-core/last/train/meta.yml
+++ b/modules/nf-core/last/train/meta.yml
@@ -42,8 +42,13 @@ output:
       type: file
       description: Trained parameter file
       pattern: "*.train"
+  - multiqc:
+      type: file
+      description: Alignment parameter summary for MultiQC
+      pattern: "*.tsv"
 authors:
   - "@aleksandrabliznina"
   - "@charles-plessy"
+  - "@U13bs1125"
 maintainers:
   - "@charles-plessy"
diff --git a/modules/nf-core/last/train/tests/main.nf.test.snap b/modules/nf-core/last/train/tests/main.nf.test.snap
index d41a8a63ded..703bcfa0152 100644
--- a/modules/nf-core/last/train/tests/main.nf.test.snap
+++ b/modules/nf-core/last/train/tests/main.nf.test.snap
@@ -12,8 +12,26 @@
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "contigs",
+                            "single_end": false
+                        },
+                        "contigs.train.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
                     "versions.yml:md5,c5578547acf9e77e1e8f6bf796e32ac2"
                 ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "contigs",
+                            "single_end": false
+                        },
+                        "contigs.train.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "param_file": [
                     [
                         {
@@ -32,7 +50,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-06T23:01:07.091657"
+        "timestamp": "2024-07-03T18:04:56.173906"
     },
     "sarscov2 - genome - contigs": {
         "content": [
@@ -47,7 +65,25 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c5578547acf9e77e1e8f6bf796e32ac2"
+                    [
+                        {
+                            "id": "contigs",
+                            "single_end": false
+                        },
+                        "contigs.train.tsv:md5,f09bcd1a111241a3439258a43c2a1a4e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,38234cf053c708e57cc080990f777411"
+                ],
+                "multiqc": [
+                    [
+                        {
+                            "id": "contigs",
+                            "single_end": false
+                        },
+                        "contigs.train.tsv:md5,f09bcd1a111241a3439258a43c2a1a4e"
+                    ]
                 ],
                 "param_file": [
                     [
@@ -59,7 +95,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c5578547acf9e77e1e8f6bf796e32ac2"
+                    "versions.yml:md5,38234cf053c708e57cc080990f777411"
                 ]
             }
         ],
@@ -67,6 +103,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-06T23:00:45.493868"
+        "timestamp": "2024-07-03T18:04:34.914789"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/lofreq/callparallel/main.nf b/modules/nf-core/lofreq/callparallel/main.nf
index 8d4f8af638f..b28fa3c7155 100644
--- a/modules/nf-core/lofreq/callparallel/main.nf
+++ b/modules/nf-core/lofreq/callparallel/main.nf
@@ -8,9 +8,9 @@ process LOFREQ_CALLPARALLEL {
         'biocontainers/lofreq:2.1.5--py38h588ecb2_4' }"
 
     input:
-    tuple val(meta), path(bam), path(bai), path(intervals)
-    path fasta
-    path fai
+    tuple val(meta) , path(bam), path(bai), path(intervals)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
@@ -23,7 +23,21 @@ process LOFREQ_CALLPARALLEL {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def options_intervals = intervals ? "-l ${intervals}" : ""
+
+    def alignment_cram =  bam.Extension == "cram" ? true : false
+    def alignment_bam = bam.Extension == "bam" ? true : false
+    def alignment_out = alignment_cram ? bam.BaseName + ".bam" : "${bam}"
+
+    def samtools_cram_convert = ''
+    samtools_cram_convert += alignment_cram ? "    samtools view -T ${fasta} ${bam} -@ $task.cpus -o ${alignment_out}\n" : ''
+    samtools_cram_convert += alignment_cram ? "    samtools index ${alignment_out}\n" : ''
+
+    def samtools_cram_remove = ''
+    samtools_cram_remove += alignment_cram ? "     rm ${alignment_out}\n" : ''
+    samtools_cram_remove += alignment_cram ? "     rm ${alignment_out}.bai\n " : ''
     """
+    $samtools_cram_convert
+
     lofreq \\
         call-parallel \\
         --pp-threads $task.cpus \\
@@ -31,7 +45,20 @@ process LOFREQ_CALLPARALLEL {
         $options_intervals \\
         -f $fasta \\
         -o ${prefix}.vcf.gz \\
-        $bam
+        $alignment_out
+
+    $samtools_cram_remove
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        lofreq: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "" | gzip > ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/lofreq/callparallel/meta.yml b/modules/nf-core/lofreq/callparallel/meta.yml
index bfe862acb6f..21c4f037f7d 100644
--- a/modules/nf-core/lofreq/callparallel/meta.yml
+++ b/modules/nf-core/lofreq/callparallel/meta.yml
@@ -20,20 +20,30 @@ input:
         e.g. [ id:'test' ]
   - bam:
       type: file
-      description: Sorted BAM file
+      description: Tumor sample sorted BAM file
       pattern: "*.{bam}"
   - bai:
       type: file
       description: BAM index file
-      pattern: "*.{bai}"
+      pattern: "*.{bam.bai}"
   - intervals:
       type: file
       description: BED file containing target regions for variant calling
       pattern: "*.{bed}"
+  - meta2:
+      type: map
+      description: |
+        Groovy Map containing sample information about the reference fasta
+        e.g. [ id:'reference' ]
   - fasta:
       type: file
       description: Reference genome FASTA file
       pattern: "*.{fasta}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing sample information about the reference fasta fai
+        e.g. [ id:'reference' ]
   - fai:
       type: file
       description: Reference genome FASTA index file
@@ -58,3 +68,5 @@ authors:
 maintainers:
   - "@kaurravneet4123"
   - "@bjohnnyd"
+  - "@nevinwu"
+  - "@AitorPeseta"
diff --git a/modules/nf-core/lofreq/callparallel/tests/main.nf.test b/modules/nf-core/lofreq/callparallel/tests/main.nf.test
new file mode 100644
index 00000000000..9df2b30ec47
--- /dev/null
+++ b/modules/nf-core/lofreq/callparallel/tests/main.nf.test
@@ -0,0 +1,103 @@
+nextflow_process {
+
+    name "Test Process LOFREQ_CALLPARALLEL"
+    script "../main.nf"
+    process "LOFREQ_CALLPARALLEL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "lofreq"
+    tag "lofreq/callparallel"
+
+    test("sarscov2 - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                        []
+                        ]
+                input[1] = [ [ id:'fasta' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                        ]
+                input[2] = [ [ id:'fai' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains('##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">') }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - bed") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                        ]
+                input[1] = [ [ id:'fasta' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                        ]
+                input[2] = [ [ id:'fai' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+                { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains('##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">') }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
+                        []
+                        ]
+                input[1] = [ [ id:'fasta' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                        ]
+                input[2] = [ [ id:'fai' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+                        ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/lofreq/callparallel/tests/main.nf.test.snap b/modules/nf-core/lofreq/callparallel/tests/main.nf.test.snap
new file mode 100644
index 00000000000..2240656a9ab
--- /dev/null
+++ b/modules/nf-core/lofreq/callparallel/tests/main.nf.test.snap
@@ -0,0 +1,59 @@
+{
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,56d45e0015add277b2689f071a4fe3e4"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,56d45e0015add277b2689f071a4fe3e4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T12:57:00.731035"
+    },
+    "sarscov2 - bam": {
+        "content": [
+            [
+                "versions.yml:md5,56d45e0015add277b2689f071a4fe3e4"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T12:59:23.105421"
+    },
+    "sarscov2 - bam - bed": {
+        "content": [
+            [
+                "versions.yml:md5,56d45e0015add277b2689f071a4fe3e4"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T12:59:28.355632"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/lofreq/callparallel/tests/tags.yml b/modules/nf-core/lofreq/callparallel/tests/tags.yml
new file mode 100644
index 00000000000..14c36bc2745
--- /dev/null
+++ b/modules/nf-core/lofreq/callparallel/tests/tags.yml
@@ -0,0 +1,2 @@
+lofreq/callparallel:
+  - "modules/nf-core/lofreq/callparallel/**"
diff --git a/modules/nf-core/lofreq/somatic/main.nf b/modules/nf-core/lofreq/somatic/main.nf
index cab72f8c003..cc57367b562 100644
--- a/modules/nf-core/lofreq/somatic/main.nf
+++ b/modules/nf-core/lofreq/somatic/main.nf
@@ -1,14 +1,13 @@
 process LOFREQ_SOMATIC {
     tag "$meta.id"
-    label "process_high"
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/lofreq:2.1.5--py38h588ecb2_4' :
         'biocontainers/lofreq:2.1.5--py38h588ecb2_4' }"
-
     input:
-    tuple val(meta), path(tumor_bam), path(tumor_bai), path(normal_bam), path(normal_bai), path(target_bed)
+    tuple val(meta), path(tumor), path(tumor_index), path(normal), path(normal_index), path(target_bed)
     tuple val(meta2), path(fasta)
     tuple val(meta3), path(fai)
 
@@ -23,17 +22,39 @@ process LOFREQ_SOMATIC {
     def args = task.ext.args ?: ""
     def prefix = task.ext.prefix ?: "${meta.id}"
     def options_target_bed = target_bed ? "-l ${target_bed}" : ""
+
+    def tumor_cram =  tumor.Extension == "cram" ? true : false
+    def normal_cram =  normal.Extension == "cram" ? true : false
+
+    def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"
+    def normal_out = normal_cram ? normal.BaseName + ".bam" : "${normal}"
+
+    def samtools_cram_convert = ''
+    samtools_cram_convert += normal_cram ? "    samtools view -T $fasta $normal -@ $task.cpus -o $normal_out\n" : ''
+    samtools_cram_convert += normal_cram ? "    samtools index $normal_out\n" : ''
+    samtools_cram_convert += tumor_cram ? "    samtools view -T ${fasta} $tumor -@ $task.cpus -o $tumor_out\n" : ''
+    samtools_cram_convert += tumor_cram ? "    samtools index ${tumor_out}\n" : ''
+
+    def samtools_cram_remove = ''
+    samtools_cram_remove += tumor_cram ? "     rm $tumor_out\n" : ''
+    samtools_cram_remove += tumor_cram ? "     rm ${tumor_out}.bai\n " : ''
+    samtools_cram_remove += normal_cram ? "     rm $normal_out\n" : ''
+    samtools_cram_remove += normal_cram ? "     rm ${normal_out}.bai\n " : ''
     """
+    $samtools_cram_convert
+
     lofreq \\
         somatic \\
         --threads $task.cpus \\
         $args \\
         -f $fasta \\
-        -t $tumor_bam \\
-        -n $normal_bam \\
+        -t $tumor_out \\
+        -n $normal_out \\
         ${options_target_bed} \\
         -o ${prefix}
 
+    $samtools_cram_remove
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         lofreq: \$(echo \$(lofreq version 2>&1) | sed 's/^version: //; s/ *commit.*\$//')
@@ -43,7 +64,7 @@ process LOFREQ_SOMATIC {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.vcf.gz
+    echo "" | gzip > ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/lofreq/somatic/meta.yml b/modules/nf-core/lofreq/somatic/meta.yml
index e165312dd1e..f29b538481d 100644
--- a/modules/nf-core/lofreq/somatic/meta.yml
+++ b/modules/nf-core/lofreq/somatic/meta.yml
@@ -12,7 +12,7 @@ tools:
       homepage: https://csb5.github.io/lofreq/
       documentation: https://csb5.github.io/lofreq/commands/
       doi: 10.1093/nar/gks918
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map
@@ -23,22 +23,22 @@ input:
   - meta3:
       type: map
       description: Groovy Map containing reference information
-  - tumor_bam:
+  - tumor:
       type: file
       description: tumor sample input BAM file
       pattern: "*.{bam}"
-  - tumor_bai:
+  - tumor_index:
       type: file
       description: tumor sample BAM index file
-      pattern: "*.{bai}"
-  - normal_bam:
+      pattern: "*.{bam.bai}"
+  - normal:
       type: file
       description: normal sample input BAM file
       pattern: "*.{bam}"
-  - normal_bai:
+  - normal_index:
       type: file
       description: normal sample BAM index file
-      pattern: "*.{bai}"
+      pattern: "*.{bam.bai}"
   - fasta:
       type: file
       description: Reference genome FASTA file
@@ -69,3 +69,4 @@ authors:
   - "@nevinwu"
 maintainers:
   - "@nevinwu"
+  - "@AitorPeseta"
diff --git a/modules/nf-core/lofreq/somatic/tests/main.nf.test b/modules/nf-core/lofreq/somatic/tests/main.nf.test
new file mode 100644
index 00000000000..4109fee3f60
--- /dev/null
+++ b/modules/nf-core/lofreq/somatic/tests/main.nf.test
@@ -0,0 +1,87 @@
+nextflow_process {
+
+    name "Test Process LOFREQ_SOMATIC"
+    script "../main.nf"
+    process "LOFREQ_SOMATIC"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "lofreq"
+    tag "lofreq/somatic"
+
+    test("human - bam") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'human' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'human' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.vcf[0][1][1]).linesGzip.toString().contains('##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).') },
+                { assert snapshot(
+                    process.out.vcf[0][1].size(),
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("human - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'human' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'human' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/lofreq/somatic/tests/main.nf.test.snap b/modules/nf-core/lofreq/somatic/tests/main.nf.test.snap
new file mode 100644
index 00000000000..d3aaaad89bc
--- /dev/null
+++ b/modules/nf-core/lofreq/somatic/tests/main.nf.test.snap
@@ -0,0 +1,48 @@
+{
+    "human - bam - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1794e4641324dc7d748047586b077fe8"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1794e4641324dc7d748047586b077fe8"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T10:37:58.931241788"
+    },
+    "human - bam": {
+        "content": [
+            10,
+            [
+                "versions.yml:md5,1794e4641324dc7d748047586b077fe8"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T10:57:24.957448368"
+    }
+}
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
index ecb7dd7b281..2121492d6fd 100644
--- a/modules/nf-core/multiqc/environment.yml
+++ b/modules/nf-core/multiqc/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::multiqc=1.22.3
+  - bioconda::multiqc=1.23
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 2581a4963ad..ac624e86988 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -3,8 +3,8 @@ process MULTIQC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.22.3--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.22.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.23--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.23--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
index 0a4760e42f7..45e95e5dea0 100644
--- a/modules/nf-core/multiqc/tests/main.nf.test.snap
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "multiqc_versions_single": {
         "content": [
             [
-                "versions.yml:md5,bf3b209659477254bb8fa5a9405f9984"
+                "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-25T12:31:21.878452033"
+        "timestamp": "2024-07-10T12:41:34.562023"
     },
     "multiqc_stub": {
         "content": [
@@ -17,25 +17,25 @@
                 "multiqc_report.html",
                 "multiqc_data",
                 "multiqc_plots",
-                "versions.yml:md5,bf3b209659477254bb8fa5a9405f9984"
+                "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-25T12:32:02.322196503"
+        "timestamp": "2024-07-10T11:27:11.933869532"
     },
     "multiqc_versions_config": {
         "content": [
             [
-                "versions.yml:md5,bf3b209659477254bb8fa5a9405f9984"
+                "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-25T12:31:50.064227638"
+        "timestamp": "2024-07-10T11:26:56.709849369"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/nanoq/main.nf b/modules/nf-core/nanoq/main.nf
index 298ede2b7bc..6d35a4073ad 100644
--- a/modules/nf-core/nanoq/main.nf
+++ b/modules/nf-core/nanoq/main.nf
@@ -12,8 +12,8 @@ process NANOQ {
     val(output_format) //One of the following: fastq, fastq.gz, fastq.bz2, fastq.lzma, fasta, fasta.gz, fasta.bz2, fasta.lzma.
 
     output:
-    tuple val(meta), path("*.stats")                                                  , emit: stats
-    tuple val(meta), path("*_nanoq.${output_format}")                                 , emit: reads
+    tuple val(meta), path("*.{stats,json}")                                           , emit: stats
+    tuple val(meta), path("*_filtered.${output_format}")                              , emit: reads
     path "versions.yml"                                                               , emit: versions
 
     when:
@@ -21,9 +21,10 @@ process NANOQ {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}_nanoq"
+    def prefix = task.ext.prefix ?: "${meta.id}_filtered"
     """
     nanoq -i $ontreads \\
+        ${args} \\
         -r ${prefix}.stats \\
         -o ${prefix}.$output_format
 
@@ -35,7 +36,7 @@ process NANOQ {
 
     stub:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}_nanoq"
+    def prefix = task.ext.prefix ?: "${meta.id}_filtered"
     """
     echo "" | gzip > ${prefix}.$output_format
     touch ${prefix}.stats
diff --git a/modules/nf-core/nanoq/meta.yml b/modules/nf-core/nanoq/meta.yml
index 87fd2f41d9e..85c0c9789a1 100644
--- a/modules/nf-core/nanoq/meta.yml
+++ b/modules/nf-core/nanoq/meta.yml
@@ -42,7 +42,7 @@ output:
   - stats:
       type: file
       description: Summary report of reads statistics.
-      pattern: "*.stats"
+      pattern: "*.{stats,json}"
 
   - reads:
       type: file
diff --git a/modules/nf-core/nanoq/tests/main.nf.test.snap b/modules/nf-core/nanoq/tests/main.nf.test.snap
index e9f6b8b5453..b5dda2a7871 100644
--- a/modules/nf-core/nanoq/tests/main.nf.test.snap
+++ b/modules/nf-core/nanoq/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -17,7 +17,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.gz:md5,7567d853ada6ac142332619d0b541d76"
+                        "test_filtered.fastq.gz:md5,7567d853ada6ac142332619d0b541d76"
                     ]
                 ],
                 "2": [
@@ -29,7 +29,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.gz:md5,7567d853ada6ac142332619d0b541d76"
+                        "test_filtered.fastq.gz:md5,7567d853ada6ac142332619d0b541d76"
                     ]
                 ],
                 "stats": [
@@ -38,7 +38,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -50,7 +50,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-07-02T10:00:12.328317"
+        "timestamp": "2024-07-11T11:39:32.117229"
     },
     "sarscov2 - nanopore_compressed_gz - stub": {
         "content": [
@@ -61,7 +61,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_filtered.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -70,7 +70,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test_filtered.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "2": [
@@ -82,7 +82,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test_filtered.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "stats": [
@@ -91,7 +91,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test_filtered.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -103,7 +103,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-07-02T10:00:24.873908"
+        "timestamp": "2024-07-11T11:42:06.039307"
     },
     "sarscov2 - nanopore_compressed_bz2": {
         "content": [
@@ -114,7 +114,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -123,7 +123,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b"
+                        "test_filtered.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b"
                     ]
                 ],
                 "2": [
@@ -135,7 +135,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b"
+                        "test_filtered.fastq.bz2:md5,b53cf14fd4eb5b16c459c41f03cc8a4b"
                     ]
                 ],
                 "stats": [
@@ -144,7 +144,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -156,7 +156,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-07-02T10:00:16.460467"
+        "timestamp": "2024-07-11T11:39:36.674647"
     },
     "sarscov2 - nanopore_compressed_lzma": {
         "content": [
@@ -167,7 +167,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -176,7 +176,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.lzma:md5,65dda701689f913734dc245b68c89e07"
+                        "test_filtered.fastq.lzma:md5,65dda701689f913734dc245b68c89e07"
                     ]
                 ],
                 "2": [
@@ -188,7 +188,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq.lzma:md5,65dda701689f913734dc245b68c89e07"
+                        "test_filtered.fastq.lzma:md5,65dda701689f913734dc245b68c89e07"
                     ]
                 ],
                 "stats": [
@@ -197,7 +197,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -209,7 +209,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-07-02T10:00:20.825269"
+        "timestamp": "2024-07-11T11:39:41.51344"
     },
     "sarscov2 - nanopore_uncompressed": {
         "content": [
@@ -220,7 +220,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "1": [
@@ -229,7 +229,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq:md5,7567d853ada6ac142332619d0b541d76"
+                        "test_filtered.fastq:md5,7567d853ada6ac142332619d0b541d76"
                     ]
                 ],
                 "2": [
@@ -241,7 +241,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.fastq:md5,7567d853ada6ac142332619d0b541d76"
+                        "test_filtered.fastq:md5,7567d853ada6ac142332619d0b541d76"
                     ]
                 ],
                 "stats": [
@@ -250,7 +250,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test_nanoq.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
+                        "test_filtered.stats:md5,5ab32af3352dfeca8268e10edf6e4dbe"
                     ]
                 ],
                 "versions": [
@@ -262,6 +262,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.1"
         },
-        "timestamp": "2024-07-02T10:00:07.8772"
+        "timestamp": "2024-07-11T11:39:26.868897"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/narfmap/align/main.nf b/modules/nf-core/narfmap/align/main.nf
index 3b91375a200..68001973bd9 100644
--- a/modules/nf-core/narfmap/align/main.nf
+++ b/modules/nf-core/narfmap/align/main.nf
@@ -2,7 +2,6 @@ process NARFMAP_ALIGN {
     tag "$meta.id"
     label 'process_high'
 
-    // TODO Add a singularity image
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'oras://community.wave.seqera.io/library/narfmap_align:8bad41386eab9997':
@@ -11,6 +10,7 @@ process NARFMAP_ALIGN {
     input:
     tuple val(meta) , path(reads)
     tuple val(meta2), path(hashmap)
+    tuple val(meta3), path(fasta)
     val   sort_bam
 
     output:
@@ -25,8 +25,13 @@ process NARFMAP_ALIGN {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reads_command = meta.single_end ? "-1 $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
-    def samtools_command = sort_bam ? 'sort' : 'view'
+    def reads_command       = meta.single_end ? "-1 $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
+    def samtools_command    = sort_bam ? 'sort' : 'view'
+    def extension_pattern   = /(--output-fmt|-O)+\s+(\S+)/
+    def extension_matcher   =  (args2 =~ extension_pattern)
+    def extension           = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
+    def reference           = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
+    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
 
     """
     dragen-os \\
@@ -35,7 +40,7 @@ process NARFMAP_ALIGN {
         --num-threads $task.cpus \\
         $reads_command \\
         2> >(tee ${prefix}.narfmap.log >&2) \\
-        | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
+        | samtools $samtools_command $args2 --threads $task.cpus ${reference} -o ${prefix}.${extension} -
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -46,9 +51,27 @@ process NARFMAP_ALIGN {
     """
 
     stub:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def reads_command = meta.single_end ? "-1 $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
+    def samtools_command = sort_bam ? 'sort' : 'view'
+    def extension_pattern = /(--output-fmt|-O)+\s+(\S+)/
+    def extension_matcher =  (args2 =~ extension_pattern)
+    def extension = extension_matcher.getCount() > 0 ? extension_matcher[0][2].toLowerCase() : "bam"
+    def reference = fasta && extension=="cram"  ? "--reference ${fasta}" : ""
+    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
+
+    def create_index = ""
+    if (extension == "cram") {
+        create_index = "touch ${prefix}.crai"
+    } else if (extension == "bam") {
+        create_index = "touch ${prefix}.csi"
+    }
+
     """
-    touch ${prefix}.bam
+    touch ${prefix}.${extension}
+    ${create_index}
     touch ${prefix}.log
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/narfmap/align/tests/main.nf.test b/modules/nf-core/narfmap/align/tests/main.nf.test
index a55cf5bf35c..367e945184f 100644
--- a/modules/nf-core/narfmap/align/tests/main.nf.test
+++ b/modules/nf-core/narfmap/align/tests/main.nf.test
@@ -33,7 +33,8 @@ nextflow_process {
                     file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
-                input[2] = false //sort
+                input[2] = [[:],[]]
+                input[3] = false //sort
                 """
             }
         }
@@ -76,7 +77,8 @@ nextflow_process {
                     file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
-                input[2] = true //sort
+                input[2] = [[:],[]]
+                input[3] = true //sort
                 """
             }
         }
@@ -122,7 +124,8 @@ nextflow_process {
                     ]
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
-                input[2] = false //sort
+                input[2] = [[:],[]]
+                input[3] = false //sort
                 """
             }
         }
@@ -168,7 +171,8 @@ nextflow_process {
                     ]
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
-                input[2] = true //sort
+                input[2] = [[:],[]]
+                input[3] = true //sort
                 """
             }
         }
@@ -214,7 +218,8 @@ nextflow_process {
                     ]
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
-                input[2] = true //sort
+                input[2] = [[:],[]]
+                input[3] = true //sort
                 """
             }
         }
@@ -261,7 +266,8 @@ nextflow_process {
                     ]
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
-                input[2] = true //sort
+                input[2] = [[:],[]]
+                input[3] = true //sort
                 """
             }
         }
@@ -278,4 +284,51 @@ nextflow_process {
             )
         }
     }
+
+    test("sarscov2 - CRAM") {
+
+        setup {
+            run("NARFMAP_HASHTABLE") {
+                script "../../hashtable/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [id:'test'],
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                ]
+                input[1] = NARFMAP_HASHTABLE.out.hashmap
+                input[2] = [[id: 'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
+                input[3] = true //sort
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    process.out.cram,
+                    process.out.csi,
+                    process.out.crai,
+                    process.out.versions,
+                    file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
+                ).match()
+                }
+            )
+        }
+
+    }
+
 }
diff --git a/modules/nf-core/narfmap/align/tests/main.nf.test.snap b/modules/nf-core/narfmap/align/tests/main.nf.test.snap
index 527a6df508c..fbf14bddf34 100644
--- a/modules/nf-core/narfmap/align/tests/main.nf.test.snap
+++ b/modules/nf-core/narfmap/align/tests/main.nf.test.snap
@@ -52,6 +52,29 @@
         },
         "timestamp": "2024-07-08T12:31:44.736492735"
     },
+    "sarscov2 - CRAM": {
+        "content": [
+            null,
+            null,
+            null,
+            [
+                "versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
+            ],
+            [
+                "decompHashTableCtxInit...",
+                "decompHashTableHeader...",
+                "decompHashTableLiterals...",
+                "decompHashTableExtIndex...",
+                "decompHashTableAutoHits...",
+                "decompHashTableSetFlags..."
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-09T14:58:38.514332124"
+    },
     "sarscov2 - fastq, hashtable, false": {
         "content": [
             [
diff --git a/modules/nf-core/narfmap/align/tests/segfault.nf.test b/modules/nf-core/narfmap/align/tests/segfault.nf.test
index 05ef3c9b530..14e101d809b 100644
--- a/modules/nf-core/narfmap/align/tests/segfault.nf.test
+++ b/modules/nf-core/narfmap/align/tests/segfault.nf.test
@@ -35,7 +35,8 @@ nextflow_process {
                     file('https://raw.githubusercontent.com/nf-core/test-datasets/nascent/testdata/SRX882903_T2.fastq.gz', checkIfExists: true)
                 ]
                 input[1] = NARFMAP_HASHTABLE.out.hashmap
-                input[2] = false //sort
+                input[2] = [[:],[]]
+                input[3] = false //sort
                 """
             }
         }
diff --git a/modules/nf-core/picard/addorreplacereadgroups/environment.yml b/modules/nf-core/picard/addorreplacereadgroups/environment.yml
index d7d2c6c0317..5c6ba553074 100644
--- a/modules/nf-core/picard/addorreplacereadgroups/environment.yml
+++ b/modules/nf-core/picard/addorreplacereadgroups/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf
index 4300ba7f8cf..3f03c6808a5 100644
--- a/modules/nf-core/picard/addorreplacereadgroups/main.nf
+++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf
@@ -4,8 +4,8 @@ process PICARD_ADDORREPLACEREADGROUPS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap
index 63a55843cee..f823197d284 100644
--- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap
+++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap
@@ -3,14 +3,14 @@
         "content": [
             "test.replaced.cram",
             [
-                "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891"
+                "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-21T12:05:47.668865"
+        "timestamp": "2024-07-10T09:54:40.471730168"
     },
     "sarscov2 - bam - stub": {
         "content": [
@@ -30,7 +30,7 @@
                     
                 ],
                 "3": [
-                    "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891"
+                    "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
                 ],
                 "bai": [
                     
@@ -47,28 +47,28 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891"
+                    "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-21T10:51:24.530553"
+        "timestamp": "2024-07-10T09:55:08.402649243"
     },
     "sarscov2 - bam": {
         "content": [
             "null.replaced.bam",
             "null.replaced.bai",
             [
-                "versions.yml:md5,0a6f049f94501dcf23aabfbc0e272891"
+                "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-21T12:05:29.696728"
+        "timestamp": "2024-07-10T09:54:22.239968953"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/picard/bedtointervallist/environment.yml b/modules/nf-core/picard/bedtointervallist/environment.yml
index 57368ccf754..1d12dbf858b 100644
--- a/modules/nf-core/picard/bedtointervallist/environment.yml
+++ b/modules/nf-core/picard/bedtointervallist/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/bedtointervallist/main.nf b/modules/nf-core/picard/bedtointervallist/main.nf
index 099d07d183a..2cc6cbd2f0f 100644
--- a/modules/nf-core/picard/bedtointervallist/main.nf
+++ b/modules/nf-core/picard/bedtointervallist/main.nf
@@ -4,8 +4,8 @@ process PICARD_BEDTOINTERVALLIST {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta) , path(bed)
diff --git a/modules/nf-core/picard/cleansam/environment.yml b/modules/nf-core/picard/cleansam/environment.yml
index c48cabe0ec6..0f00fd740ed 100644
--- a/modules/nf-core/picard/cleansam/environment.yml
+++ b/modules/nf-core/picard/cleansam/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf
index 4f6a91f17c4..7b95cebdc0f 100644
--- a/modules/nf-core/picard/cleansam/main.nf
+++ b/modules/nf-core/picard/cleansam/main.nf
@@ -4,8 +4,8 @@ process PICARD_CLEANSAM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/nf-core/picard/collecthsmetrics/environment.yml
index fbeab71bb90..b00842b1b73 100644
--- a/modules/nf-core/picard/collecthsmetrics/environment.yml
+++ b/modules/nf-core/picard/collecthsmetrics/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf
index 1e80b529782..a9cbafd44f2 100644
--- a/modules/nf-core/picard/collecthsmetrics/main.nf
+++ b/modules/nf-core/picard/collecthsmetrics/main.nf
@@ -4,8 +4,8 @@ process PICARD_COLLECTHSMETRICS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*')
diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
index 3d0575b395a..94713c0f965 100644
--- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
+++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
 
         then {
             def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..212]
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
             lines.remove(3)  // remove timestamp
             assertAll(
                 { assert process.success },
@@ -97,7 +97,7 @@ nextflow_process {
 
         then {
             def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..212]
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
             lines.remove(3)  // remove timestamp
             assertAll(
                 { assert process.success },
@@ -135,7 +135,7 @@ nextflow_process {
 
         then {
             def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..212]
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
             lines.remove(3)  // remove timestamp
             assertAll(
                 { assert process.success },
@@ -173,7 +173,7 @@ nextflow_process {
 
         then {
             def size = path(process.out.metrics[0][1]).size()
-            def lines = path(process.out.metrics[0][1]).readLines()[0..212]
+            def lines = path(process.out.metrics[0][1]).readLines()[0..100]
             lines.remove(3)  // remove timestamp
             assertAll(
                 { assert process.success },
diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap
index b3b477e1f01..53855d13b68 100644
--- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap
+++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "sarscov2 - bam - nofasta": {
         "content": [
             "test.CollectHsMetrics.coverage_metrics",
-            4140,
+            3548,
             [
                 "## htsjdk.samtools.metrics.StringHeader",
                 "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
@@ -10,7 +10,7 @@
                 "",
                 "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
                 "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
-                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.016027\t0\t\t\t",
+                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0.015734\t0\t\t\t",
                 "",
                 "## HISTOGRAM\tjava.lang.Integer",
                 "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
@@ -103,146 +103,34 @@
                 "86\t0\t0",
                 "87\t0\t0",
                 "88\t0\t0",
-                "89\t0\t0",
-                "90\t0\t0",
-                "91\t0\t0",
-                "92\t0\t0",
-                "93\t0\t0",
-                "94\t0\t0",
-                "95\t0\t0",
-                "96\t0\t0",
-                "97\t0\t0",
-                "98\t0\t0",
-                "99\t0\t0",
-                "100\t0\t0",
-                "101\t0\t0",
-                "102\t0\t0",
-                "103\t0\t0",
-                "104\t0\t0",
-                "105\t0\t0",
-                "106\t0\t0",
-                "107\t0\t0",
-                "108\t0\t0",
-                "109\t0\t0",
-                "110\t0\t0",
-                "111\t0\t0",
-                "112\t0\t0",
-                "113\t0\t0",
-                "114\t0\t0",
-                "115\t0\t0",
-                "116\t0\t0",
-                "117\t0\t0",
-                "118\t0\t0",
-                "119\t0\t0",
-                "120\t0\t0",
-                "121\t0\t0",
-                "122\t0\t0",
-                "123\t0\t0",
-                "124\t0\t0",
-                "125\t0\t0",
-                "126\t0\t0",
-                "127\t0\t0",
-                "128\t0\t0",
-                "129\t0\t0",
-                "130\t0\t0",
-                "131\t0\t0",
-                "132\t0\t0",
-                "133\t0\t0",
-                "134\t0\t0",
-                "135\t0\t0",
-                "136\t0\t0",
-                "137\t0\t0",
-                "138\t0\t0",
-                "139\t0\t0",
-                "140\t0\t0",
-                "141\t0\t0",
-                "142\t0\t0",
-                "143\t0\t0",
-                "144\t0\t0",
-                "145\t0\t0",
-                "146\t0\t0",
-                "147\t0\t0",
-                "148\t0\t0",
-                "149\t0\t0",
-                "150\t0\t0",
-                "151\t0\t0",
-                "152\t0\t0",
-                "153\t0\t0",
-                "154\t0\t0",
-                "155\t0\t0",
-                "156\t0\t0",
-                "157\t0\t0",
-                "158\t0\t0",
-                "159\t0\t0",
-                "160\t0\t0",
-                "161\t0\t0",
-                "162\t0\t0",
-                "163\t0\t0",
-                "164\t0\t0",
-                "165\t0\t0",
-                "166\t0\t0",
-                "167\t0\t0",
-                "168\t0\t0",
-                "169\t0\t0",
-                "170\t0\t0",
-                "171\t0\t0",
-                "172\t0\t0",
-                "173\t0\t0",
-                "174\t0\t0",
-                "175\t0\t0",
-                "176\t0\t0",
-                "177\t0\t0",
-                "178\t0\t0",
-                "179\t0\t0",
-                "180\t0\t0",
-                "181\t0\t0",
-                "182\t0\t0",
-                "183\t0\t0",
-                "184\t0\t0",
-                "185\t0\t0",
-                "186\t0\t0",
-                "187\t0\t0",
-                "188\t0\t0",
-                "189\t0\t0",
-                "190\t0\t0",
-                "191\t0\t0",
-                "192\t0\t0",
-                "193\t0\t0",
-                "194\t0\t0",
-                "195\t0\t0",
-                "196\t0\t0",
-                "197\t0\t0",
-                "198\t0\t0",
-                "199\t0\t0",
-                "200\t0\t0",
-                ""
+                "89\t0\t0"
             ],
             [
-                "versions.yml:md5,e2a565b586e0aecbb72f1f0d27df7b8d"
+                "versions.yml:md5,e390b048af294086f56621c38ebde05a"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-10T09:17:21.08792"
+        "timestamp": "2024-07-10T09:45:46.991614248"
     },
     "versions": {
         "content": [
             [
-                "versions.yml:md5,e2a565b586e0aecbb72f1f0d27df7b8d"
+                "versions.yml:md5,e390b048af294086f56621c38ebde05a"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-10T09:16:57.995147"
+        "timestamp": "2024-07-10T09:36:50.350567213"
     },
     "sarscov2 - bam - samebed": {
         "content": [
             "test.CollectHsMetrics.coverage_metrics",
-            4178,
+            3586,
             [
                 "## htsjdk.samtools.metrics.StringHeader",
                 "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/baits.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
@@ -250,7 +138,7 @@
                 "",
                 "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
                 "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
-                "baits\t158\t1\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.013782\t4.995204\t\t0\t0\t0\t0\t0\t0\t158\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t381\t1\t1\t0.985\t2.411392\t2\t3\t2\t0\t0\t0\t0.005438\t0.054487\t0.259516\t0.666655\t1.205696\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7.018506\t0\t0.394304\t2\t\t\t",
+                "baits\t158\t1\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.013782\t4.995204\t\t0\t0\t0\t0\t0\t0\t158\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t381\t1\t1\t0.985\t2.411392\t2\t3\t2\t0\t0\t0\t0.005438\t0.054487\t0.259516\t0.666655\t1.205696\t1\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7.018506\t0\t0.394337\t2\t\t\t",
                 "",
                 "## HISTOGRAM\tjava.lang.Integer",
                 "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
@@ -343,134 +231,22 @@
                 "86\t0\t0",
                 "87\t0\t0",
                 "88\t0\t0",
-                "89\t0\t0",
-                "90\t0\t0",
-                "91\t0\t0",
-                "92\t0\t0",
-                "93\t0\t0",
-                "94\t0\t0",
-                "95\t0\t0",
-                "96\t0\t0",
-                "97\t0\t0",
-                "98\t0\t0",
-                "99\t0\t0",
-                "100\t0\t0",
-                "101\t0\t0",
-                "102\t0\t0",
-                "103\t0\t0",
-                "104\t0\t0",
-                "105\t0\t0",
-                "106\t0\t0",
-                "107\t0\t0",
-                "108\t0\t0",
-                "109\t0\t0",
-                "110\t0\t0",
-                "111\t0\t0",
-                "112\t0\t0",
-                "113\t0\t0",
-                "114\t0\t0",
-                "115\t0\t0",
-                "116\t0\t0",
-                "117\t0\t0",
-                "118\t0\t0",
-                "119\t0\t0",
-                "120\t0\t0",
-                "121\t0\t0",
-                "122\t0\t0",
-                "123\t0\t0",
-                "124\t0\t0",
-                "125\t0\t0",
-                "126\t0\t0",
-                "127\t0\t0",
-                "128\t0\t0",
-                "129\t0\t0",
-                "130\t0\t0",
-                "131\t0\t0",
-                "132\t0\t0",
-                "133\t0\t0",
-                "134\t0\t0",
-                "135\t0\t0",
-                "136\t0\t0",
-                "137\t0\t0",
-                "138\t0\t0",
-                "139\t0\t0",
-                "140\t0\t0",
-                "141\t0\t0",
-                "142\t0\t0",
-                "143\t0\t0",
-                "144\t0\t0",
-                "145\t0\t0",
-                "146\t0\t0",
-                "147\t0\t0",
-                "148\t0\t0",
-                "149\t0\t0",
-                "150\t0\t0",
-                "151\t0\t0",
-                "152\t0\t0",
-                "153\t0\t0",
-                "154\t0\t0",
-                "155\t0\t0",
-                "156\t0\t0",
-                "157\t0\t0",
-                "158\t0\t0",
-                "159\t0\t0",
-                "160\t0\t0",
-                "161\t0\t0",
-                "162\t0\t0",
-                "163\t0\t0",
-                "164\t0\t0",
-                "165\t0\t0",
-                "166\t0\t0",
-                "167\t0\t0",
-                "168\t0\t0",
-                "169\t0\t0",
-                "170\t0\t0",
-                "171\t0\t0",
-                "172\t0\t0",
-                "173\t0\t0",
-                "174\t0\t0",
-                "175\t0\t0",
-                "176\t0\t0",
-                "177\t0\t0",
-                "178\t0\t0",
-                "179\t0\t0",
-                "180\t0\t0",
-                "181\t0\t0",
-                "182\t0\t0",
-                "183\t0\t0",
-                "184\t0\t0",
-                "185\t0\t0",
-                "186\t0\t0",
-                "187\t0\t0",
-                "188\t0\t0",
-                "189\t0\t0",
-                "190\t0\t0",
-                "191\t0\t0",
-                "192\t0\t0",
-                "193\t0\t0",
-                "194\t0\t0",
-                "195\t0\t0",
-                "196\t0\t0",
-                "197\t0\t0",
-                "198\t0\t0",
-                "199\t0\t0",
-                "200\t0\t0",
-                ""
+                "89\t0\t0"
             ],
             [
-                "versions.yml:md5,e2a565b586e0aecbb72f1f0d27df7b8d"
+                "versions.yml:md5,e390b048af294086f56621c38ebde05a"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-10T09:18:16.259373"
+        "timestamp": "2024-07-10T09:46:33.770516478"
     },
     "sarscov2 - bam": {
         "content": [
             "test.CollectHsMetrics.coverage_metrics",
-            4190,
+            3598,
             [
                 "## htsjdk.samtools.metrics.StringHeader",
                 "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/targets.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
@@ -478,7 +254,7 @@
                 "",
                 "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
                 "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
-                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.016027\t0\t\t\t",
+                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t",
                 "",
                 "## HISTOGRAM\tjava.lang.Integer",
                 "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
@@ -571,134 +347,22 @@
                 "86\t0\t0",
                 "87\t0\t0",
                 "88\t0\t0",
-                "89\t0\t0",
-                "90\t0\t0",
-                "91\t0\t0",
-                "92\t0\t0",
-                "93\t0\t0",
-                "94\t0\t0",
-                "95\t0\t0",
-                "96\t0\t0",
-                "97\t0\t0",
-                "98\t0\t0",
-                "99\t0\t0",
-                "100\t0\t0",
-                "101\t0\t0",
-                "102\t0\t0",
-                "103\t0\t0",
-                "104\t0\t0",
-                "105\t0\t0",
-                "106\t0\t0",
-                "107\t0\t0",
-                "108\t0\t0",
-                "109\t0\t0",
-                "110\t0\t0",
-                "111\t0\t0",
-                "112\t0\t0",
-                "113\t0\t0",
-                "114\t0\t0",
-                "115\t0\t0",
-                "116\t0\t0",
-                "117\t0\t0",
-                "118\t0\t0",
-                "119\t0\t0",
-                "120\t0\t0",
-                "121\t0\t0",
-                "122\t0\t0",
-                "123\t0\t0",
-                "124\t0\t0",
-                "125\t0\t0",
-                "126\t0\t0",
-                "127\t0\t0",
-                "128\t0\t0",
-                "129\t0\t0",
-                "130\t0\t0",
-                "131\t0\t0",
-                "132\t0\t0",
-                "133\t0\t0",
-                "134\t0\t0",
-                "135\t0\t0",
-                "136\t0\t0",
-                "137\t0\t0",
-                "138\t0\t0",
-                "139\t0\t0",
-                "140\t0\t0",
-                "141\t0\t0",
-                "142\t0\t0",
-                "143\t0\t0",
-                "144\t0\t0",
-                "145\t0\t0",
-                "146\t0\t0",
-                "147\t0\t0",
-                "148\t0\t0",
-                "149\t0\t0",
-                "150\t0\t0",
-                "151\t0\t0",
-                "152\t0\t0",
-                "153\t0\t0",
-                "154\t0\t0",
-                "155\t0\t0",
-                "156\t0\t0",
-                "157\t0\t0",
-                "158\t0\t0",
-                "159\t0\t0",
-                "160\t0\t0",
-                "161\t0\t0",
-                "162\t0\t0",
-                "163\t0\t0",
-                "164\t0\t0",
-                "165\t0\t0",
-                "166\t0\t0",
-                "167\t0\t0",
-                "168\t0\t0",
-                "169\t0\t0",
-                "170\t0\t0",
-                "171\t0\t0",
-                "172\t0\t0",
-                "173\t0\t0",
-                "174\t0\t0",
-                "175\t0\t0",
-                "176\t0\t0",
-                "177\t0\t0",
-                "178\t0\t0",
-                "179\t0\t0",
-                "180\t0\t0",
-                "181\t0\t0",
-                "182\t0\t0",
-                "183\t0\t0",
-                "184\t0\t0",
-                "185\t0\t0",
-                "186\t0\t0",
-                "187\t0\t0",
-                "188\t0\t0",
-                "189\t0\t0",
-                "190\t0\t0",
-                "191\t0\t0",
-                "192\t0\t0",
-                "193\t0\t0",
-                "194\t0\t0",
-                "195\t0\t0",
-                "196\t0\t0",
-                "197\t0\t0",
-                "198\t0\t0",
-                "199\t0\t0",
-                "200\t0\t0",
-                ""
+                "89\t0\t0"
             ],
             [
-                "versions.yml:md5,e2a565b586e0aecbb72f1f0d27df7b8d"
+                "versions.yml:md5,e390b048af294086f56621c38ebde05a"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-10T09:13:12.139682"
+        "timestamp": "2024-07-10T09:45:16.117386245"
     },
     "sarscov2 - bam - bed": {
         "content": [
             "test.CollectHsMetrics.coverage_metrics",
-            4187,
+            3595,
             [
                 "## htsjdk.samtools.metrics.StringHeader",
                 "# CollectHsMetrics --BAIT_INTERVALS baits/baits.interval_list --TARGET_INTERVALS targets/test.interval_list --INPUT test.paired_end.sorted.bam --OUTPUT test.CollectHsMetrics.coverage_metrics --REFERENCE_SEQUENCE genome.fasta --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --SAMPLE_SIZE 10000 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
@@ -706,7 +370,7 @@
                 "",
                 "## METRICS CLASS\tpicard.analysis.directed.HsMetrics",
                 "BAIT_SET\tBAIT_TERRITORY\tBAIT_DESIGN_EFFICIENCY\tON_BAIT_BASES\tNEAR_BAIT_BASES\tOFF_BAIT_BASES\tPCT_SELECTED_BASES\tPCT_OFF_BAIT\tON_BAIT_VS_SELECTED\tMEAN_BAIT_COVERAGE\tPCT_USABLE_BASES_ON_BAIT\tPCT_USABLE_BASES_ON_TARGET\tFOLD_ENRICHMENT\tHS_LIBRARY_SIZE\tHS_PENALTY_10X\tHS_PENALTY_20X\tHS_PENALTY_30X\tHS_PENALTY_40X\tHS_PENALTY_50X\tHS_PENALTY_100X\tTARGET_TERRITORY\tGENOME_SIZE\tTOTAL_READS\tPF_READS\tPF_BASES\tPF_UNIQUE_READS\tPF_UQ_READS_ALIGNED\tPF_BASES_ALIGNED\tPF_UQ_BASES_ALIGNED\tON_TARGET_BASES\tPCT_PF_READS\tPCT_PF_UQ_READS\tPCT_PF_UQ_READS_ALIGNED\tMEAN_TARGET_COVERAGE\tMEDIAN_TARGET_COVERAGE\tMAX_TARGET_COVERAGE\tMIN_TARGET_COVERAGE\tZERO_CVG_TARGETS_PCT\tPCT_EXC_DUPE\tPCT_EXC_ADAPTER\tPCT_EXC_MAPQ\tPCT_EXC_BASEQ\tPCT_EXC_OVERLAP\tPCT_EXC_OFF_TARGET\tFOLD_80_BASE_PENALTY\tPCT_TARGET_BASES_1X\tPCT_TARGET_BASES_2X\tPCT_TARGET_BASES_10X\tPCT_TARGET_BASES_20X\tPCT_TARGET_BASES_30X\tPCT_TARGET_BASES_40X\tPCT_TARGET_BASES_50X\tPCT_TARGET_BASES_100X\tPCT_TARGET_BASES_250X\tPCT_TARGET_BASES_500X\tPCT_TARGET_BASES_1000X\tPCT_TARGET_BASES_2500X\tPCT_TARGET_BASES_5000X\tPCT_TARGET_BASES_10000X\tPCT_TARGET_BASES_25000X\tPCT_TARGET_BASES_50000X\tPCT_TARGET_BASES_100000X\tAT_DROPOUT\tGC_DROPOUT\tHET_SNP_SENSITIVITY\tHET_SNP_Q\tSAMPLE\tLIBRARY\tREAD_GROUP",
-                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.016027\t0\t\t\t",
+                "baits\t158\t0.594937\t725\t3985\t22691\t0.171892\t0.828108\t0.153928\t4.588608\t0.026225\t0.000181\t4.995204\t\t0\t0\t0\t0\t0\t0\t94\t29829\t200\t200\t27645\t200\t197\t27401\t27401\t5\t1\t1\t0.985\t0.053191\t0\t1\t0\t0.75\t0\t0\t0.005438\t0.054487\t0.259516\t0.680377\t?\t0.053191\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t76.595745\t23.404255\t0.015734\t0\t\t\t",
                 "",
                 "## HISTOGRAM\tjava.lang.Integer",
                 "coverage_or_base_quality\thigh_quality_coverage_count\tunfiltered_baseq_count",
@@ -799,128 +463,16 @@
                 "86\t0\t0",
                 "87\t0\t0",
                 "88\t0\t0",
-                "89\t0\t0",
-                "90\t0\t0",
-                "91\t0\t0",
-                "92\t0\t0",
-                "93\t0\t0",
-                "94\t0\t0",
-                "95\t0\t0",
-                "96\t0\t0",
-                "97\t0\t0",
-                "98\t0\t0",
-                "99\t0\t0",
-                "100\t0\t0",
-                "101\t0\t0",
-                "102\t0\t0",
-                "103\t0\t0",
-                "104\t0\t0",
-                "105\t0\t0",
-                "106\t0\t0",
-                "107\t0\t0",
-                "108\t0\t0",
-                "109\t0\t0",
-                "110\t0\t0",
-                "111\t0\t0",
-                "112\t0\t0",
-                "113\t0\t0",
-                "114\t0\t0",
-                "115\t0\t0",
-                "116\t0\t0",
-                "117\t0\t0",
-                "118\t0\t0",
-                "119\t0\t0",
-                "120\t0\t0",
-                "121\t0\t0",
-                "122\t0\t0",
-                "123\t0\t0",
-                "124\t0\t0",
-                "125\t0\t0",
-                "126\t0\t0",
-                "127\t0\t0",
-                "128\t0\t0",
-                "129\t0\t0",
-                "130\t0\t0",
-                "131\t0\t0",
-                "132\t0\t0",
-                "133\t0\t0",
-                "134\t0\t0",
-                "135\t0\t0",
-                "136\t0\t0",
-                "137\t0\t0",
-                "138\t0\t0",
-                "139\t0\t0",
-                "140\t0\t0",
-                "141\t0\t0",
-                "142\t0\t0",
-                "143\t0\t0",
-                "144\t0\t0",
-                "145\t0\t0",
-                "146\t0\t0",
-                "147\t0\t0",
-                "148\t0\t0",
-                "149\t0\t0",
-                "150\t0\t0",
-                "151\t0\t0",
-                "152\t0\t0",
-                "153\t0\t0",
-                "154\t0\t0",
-                "155\t0\t0",
-                "156\t0\t0",
-                "157\t0\t0",
-                "158\t0\t0",
-                "159\t0\t0",
-                "160\t0\t0",
-                "161\t0\t0",
-                "162\t0\t0",
-                "163\t0\t0",
-                "164\t0\t0",
-                "165\t0\t0",
-                "166\t0\t0",
-                "167\t0\t0",
-                "168\t0\t0",
-                "169\t0\t0",
-                "170\t0\t0",
-                "171\t0\t0",
-                "172\t0\t0",
-                "173\t0\t0",
-                "174\t0\t0",
-                "175\t0\t0",
-                "176\t0\t0",
-                "177\t0\t0",
-                "178\t0\t0",
-                "179\t0\t0",
-                "180\t0\t0",
-                "181\t0\t0",
-                "182\t0\t0",
-                "183\t0\t0",
-                "184\t0\t0",
-                "185\t0\t0",
-                "186\t0\t0",
-                "187\t0\t0",
-                "188\t0\t0",
-                "189\t0\t0",
-                "190\t0\t0",
-                "191\t0\t0",
-                "192\t0\t0",
-                "193\t0\t0",
-                "194\t0\t0",
-                "195\t0\t0",
-                "196\t0\t0",
-                "197\t0\t0",
-                "198\t0\t0",
-                "199\t0\t0",
-                "200\t0\t0",
-                ""
+                "89\t0\t0"
             ],
             [
-                "versions.yml:md5,e2a565b586e0aecbb72f1f0d27df7b8d"
+                "versions.yml:md5,e390b048af294086f56621c38ebde05a"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-10T09:17:48.183631"
+        "timestamp": "2024-07-10T09:46:13.489487836"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml
index 73ba7dc6bcf..87a8c7d8055 100644
--- a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml
+++ b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/collectinsertsizemetrics/main.nf b/modules/nf-core/picard/collectinsertsizemetrics/main.nf
index 06c4bc17223..9915399269f 100644
--- a/modules/nf-core/picard/collectinsertsizemetrics/main.nf
+++ b/modules/nf-core/picard/collectinsertsizemetrics/main.nf
@@ -4,8 +4,8 @@ process PICARD_COLLECTINSERTSIZEMETRICS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/collectmultiplemetrics/environment.yml b/modules/nf-core/picard/collectmultiplemetrics/environment.yml
index 79b33280653..6a16f00dcc6 100644
--- a/modules/nf-core/picard/collectmultiplemetrics/environment.yml
+++ b/modules/nf-core/picard/collectmultiplemetrics/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf
index 5640ce9411f..c5555871dc3 100644
--- a/modules/nf-core/picard/collectmultiplemetrics/main.nf
+++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf
@@ -4,8 +4,8 @@ process PICARD_COLLECTMULTIPLEMETRICS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta) , path(bam), path(bai)
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml
index 542b2e823fe..1dfb9654889 100644
--- a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml
+++ b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/collectrnaseqmetrics/main.nf b/modules/nf-core/picard/collectrnaseqmetrics/main.nf
index f833a105c84..0c8f2cfa2c1 100644
--- a/modules/nf-core/picard/collectrnaseqmetrics/main.nf
+++ b/modules/nf-core/picard/collectrnaseqmetrics/main.nf
@@ -4,8 +4,8 @@ process PICARD_COLLECTRNASEQMETRICS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/collectwgsmetrics/environment.yml b/modules/nf-core/picard/collectwgsmetrics/environment.yml
index 6a0b9258e0f..9f87553465b 100644
--- a/modules/nf-core/picard/collectwgsmetrics/environment.yml
+++ b/modules/nf-core/picard/collectwgsmetrics/environment.yml
@@ -4,5 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
   - r::r-base
diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf
index 35f4129cfb2..6002a7ca95c 100644
--- a/modules/nf-core/picard/collectwgsmetrics/main.nf
+++ b/modules/nf-core/picard/collectwgsmetrics/main.nf
@@ -4,8 +4,8 @@ process PICARD_COLLECTWGSMETRICS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/picard/createsequencedictionary/environment.yml b/modules/nf-core/picard/createsequencedictionary/environment.yml
index f3554628b84..48a31a26dcc 100644
--- a/modules/nf-core/picard/createsequencedictionary/environment.yml
+++ b/modules/nf-core/picard/createsequencedictionary/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf
index a1eb8bed5c4..bc925a0dedc 100644
--- a/modules/nf-core/picard/createsequencedictionary/main.nf
+++ b/modules/nf-core/picard/createsequencedictionary/main.nf
@@ -4,8 +4,8 @@ process PICARD_CREATESEQUENCEDICTIONARY {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/picard/crosscheckfingerprints/environment.yml b/modules/nf-core/picard/crosscheckfingerprints/environment.yml
index ab81a3dceb1..5df18044c3c 100644
--- a/modules/nf-core/picard/crosscheckfingerprints/environment.yml
+++ b/modules/nf-core/picard/crosscheckfingerprints/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf
index 50e0376c266..f6df55ade7b 100644
--- a/modules/nf-core/picard/crosscheckfingerprints/main.nf
+++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf
@@ -4,8 +4,8 @@ process PICARD_CROSSCHECKFINGERPRINTS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta),  path(input1), path(input1_index), path(input2), path(input2_index), path(haplotype_map)
diff --git a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap
index 96fbdc845d4..f283f13305f 100644
--- a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap
+++ b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap
@@ -22,25 +22,25 @@
     "Crosscheck versions stub": {
         "content": [
             [
-                "versions.yml:md5,bd0a3212a131aee499cb7f954aeac63c"
+                "versions.yml:md5,4c5a7212fc3d33ef2693462e3b792b89"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-08T14:36:24.83939"
+        "timestamp": "2024-07-10T09:57:33.939689662"
     },
     "Crosscheck versions - bam": {
         "content": [
             [
-                "versions.yml:md5,bd0a3212a131aee499cb7f954aeac63c"
+                "versions.yml:md5,4c5a7212fc3d33ef2693462e3b792b89"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-08T14:30:50.311883"
+        "timestamp": "2024-07-10T09:57:08.745266455"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/picard/extractfingerprint/environment.yml b/modules/nf-core/picard/extractfingerprint/environment.yml
index 40429b416b3..b6d7eef616c 100644
--- a/modules/nf-core/picard/extractfingerprint/environment.yml
+++ b/modules/nf-core/picard/extractfingerprint/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/extractfingerprint/main.nf b/modules/nf-core/picard/extractfingerprint/main.nf
index c10c3847ead..68b53233045 100644
--- a/modules/nf-core/picard/extractfingerprint/main.nf
+++ b/modules/nf-core/picard/extractfingerprint/main.nf
@@ -4,8 +4,8 @@ process PICARD_EXTRACTFINGERPRINT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
diff --git a/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap b/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap
index fe61840bcc6..a754ef93e28 100644
--- a/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap
+++ b/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap
@@ -2,15 +2,23 @@
     "versions": {
         "content": [
             [
-                "versions.yml:md5,90dca36c10677c9d6ad5ef7e42c4d788"
+                "versions.yml:md5,cbf898a998bb9b90d2e4110ee343d674"
             ]
         ],
-        "timestamp": "2023-12-04T15:53:39.112154"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-10T09:53:08.359314244"
     },
     "extract_fingerprint": {
         "content": [
             "##fileformat=VCFv4.2"
         ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
         "timestamp": "2023-12-04T15:53:39.12594"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/picard/fastqtosam/environment.yml b/modules/nf-core/picard/fastqtosam/environment.yml
index 1912c391791..4c97b78f329 100644
--- a/modules/nf-core/picard/fastqtosam/environment.yml
+++ b/modules/nf-core/picard/fastqtosam/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf
index eac5b947f9d..dedd70a0318 100644
--- a/modules/nf-core/picard/fastqtosam/main.nf
+++ b/modules/nf-core/picard/fastqtosam/main.nf
@@ -4,8 +4,8 @@ process PICARD_FASTQTOSAM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/picard/filtersamreads/environment.yml b/modules/nf-core/picard/filtersamreads/environment.yml
index 3fe7207ce64..88248ad425e 100644
--- a/modules/nf-core/picard/filtersamreads/environment.yml
+++ b/modules/nf-core/picard/filtersamreads/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf
index f64e4a05d63..32977bdc306 100644
--- a/modules/nf-core/picard/filtersamreads/main.nf
+++ b/modules/nf-core/picard/filtersamreads/main.nf
@@ -4,8 +4,8 @@ process PICARD_FILTERSAMREADS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam), path(readlist)
diff --git a/modules/nf-core/picard/fixmateinformation/environment.yml b/modules/nf-core/picard/fixmateinformation/environment.yml
index 890c13a2aa9..cf197ce646f 100644
--- a/modules/nf-core/picard/fixmateinformation/environment.yml
+++ b/modules/nf-core/picard/fixmateinformation/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf
index 85519558a6c..bf29e24cc07 100644
--- a/modules/nf-core/picard/fixmateinformation/main.nf
+++ b/modules/nf-core/picard/fixmateinformation/main.nf
@@ -4,8 +4,8 @@ process PICARD_FIXMATEINFORMATION {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/liftovervcf/environment.yml b/modules/nf-core/picard/liftovervcf/environment.yml
index e953ec958cf..16dd9f61307 100644
--- a/modules/nf-core/picard/liftovervcf/environment.yml
+++ b/modules/nf-core/picard/liftovervcf/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf
index ab7212a101a..e47b74f787e 100644
--- a/modules/nf-core/picard/liftovervcf/main.nf
+++ b/modules/nf-core/picard/liftovervcf/main.nf
@@ -4,8 +4,8 @@ process PICARD_LIFTOVERVCF {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml
index 58b795f54a8..a27db11865c 100644
--- a/modules/nf-core/picard/markduplicates/environment.yml
+++ b/modules/nf-core/picard/markduplicates/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf
index ad0b296361b..cf18ac35ca9 100644
--- a/modules/nf-core/picard/markduplicates/main.nf
+++ b/modules/nf-core/picard/markduplicates/main.nf
@@ -4,8 +4,8 @@ process PICARD_MARKDUPLICATES {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap
index eb17111e4c5..24a57d0e3e0 100644
--- a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap
+++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "sorted_bam_versions": {
         "content": [
             [
-                "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17"
+                "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-20T15:31:50.928021"
+        "timestamp": "2024-07-10T09:49:13.838237323"
     },
     "unsorted_bam_name": {
         "content": [
@@ -25,29 +25,29 @@
         "content": [
             [
                 "## htsjdk.samtools.metrics.StringHeader",
-                "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
+                "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
                 "## htsjdk.samtools.metrics.StringHeader"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-20T15:25:47.518152"
+        "timestamp": "2024-07-10T09:49:32.685023439"
     },
     "sorted_bam_metrics": {
         "content": [
             [
                 "## htsjdk.samtools.metrics.StringHeader",
-                "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
+                "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
                 "## htsjdk.samtools.metrics.StringHeader"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-21T11:39:10.318331"
+        "timestamp": "2024-07-10T09:49:13.788936246"
     },
     "cram_name": {
         "content": [
@@ -62,40 +62,40 @@
     "cram_versions": {
         "content": [
             [
-                "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17"
+                "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-01-19T10:27:03.26989"
+        "timestamp": "2024-07-10T09:49:32.731312566"
     },
     "unsorted_bam_versions": {
         "content": [
             [
-                "versions.yml:md5,b699af51b1956f3810f8a7c066e0ab17"
+                "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-20T15:31:24.040403"
+        "timestamp": "2024-07-10T09:48:57.466503381"
     },
     "unsorted_bam_metrics": {
         "content": [
             [
                 "## htsjdk.samtools.metrics.StringHeader",
-                "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
+                "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false",
                 "## htsjdk.samtools.metrics.StringHeader"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-03-21T10:51:12.831787"
+        "timestamp": "2024-07-10T09:48:57.387579606"
     },
     "sorted_bam_name": {
         "content": [
diff --git a/modules/nf-core/picard/mergesamfiles/environment.yml b/modules/nf-core/picard/mergesamfiles/environment.yml
index c3bffb0c070..af6a04a1613 100644
--- a/modules/nf-core/picard/mergesamfiles/environment.yml
+++ b/modules/nf-core/picard/mergesamfiles/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf
index 8044ab207b8..1e6e2274b9f 100644
--- a/modules/nf-core/picard/mergesamfiles/main.nf
+++ b/modules/nf-core/picard/mergesamfiles/main.nf
@@ -4,8 +4,8 @@ process PICARD_MERGESAMFILES {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bams)
diff --git a/modules/nf-core/picard/renamesampleinvcf/environment.yml b/modules/nf-core/picard/renamesampleinvcf/environment.yml
index 3e7d8eb5a64..b7ccb0089f3 100644
--- a/modules/nf-core/picard/renamesampleinvcf/environment.yml
+++ b/modules/nf-core/picard/renamesampleinvcf/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf
index d44b1829c48..3e4f38caa3c 100644
--- a/modules/nf-core/picard/renamesampleinvcf/main.nf
+++ b/modules/nf-core/picard/renamesampleinvcf/main.nf
@@ -5,8 +5,8 @@ process PICARD_RENAMESAMPLEINVCF {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/modules/nf-core/picard/scatterintervalsbyns/environment.yml b/modules/nf-core/picard/scatterintervalsbyns/environment.yml
index 9adb3b2529a..b36f96bf1ce 100644
--- a/modules/nf-core/picard/scatterintervalsbyns/environment.yml
+++ b/modules/nf-core/picard/scatterintervalsbyns/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/scatterintervalsbyns/main.nf b/modules/nf-core/picard/scatterintervalsbyns/main.nf
index ebd2a66bcae..344284804a1 100644
--- a/modules/nf-core/picard/scatterintervalsbyns/main.nf
+++ b/modules/nf-core/picard/scatterintervalsbyns/main.nf
@@ -4,8 +4,8 @@ process PICARD_SCATTERINTERVALSBYNS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/nf-core/picard/sortsam/environment.yml b/modules/nf-core/picard/sortsam/environment.yml
index 5fee08c1480..967b9f9f567 100644
--- a/modules/nf-core/picard/sortsam/environment.yml
+++ b/modules/nf-core/picard/sortsam/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf
index 513a23f32d0..af23e294bed 100644
--- a/modules/nf-core/picard/sortsam/main.nf
+++ b/modules/nf-core/picard/sortsam/main.nf
@@ -4,8 +4,8 @@ process PICARD_SORTSAM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/nf-core/picard/sortvcf/environment.yml b/modules/nf-core/picard/sortvcf/environment.yml
index f1dbb6b9317..a2f96e80fd3 100644
--- a/modules/nf-core/picard/sortvcf/environment.yml
+++ b/modules/nf-core/picard/sortvcf/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::picard=3.1.1
+  - bioconda::picard=3.2.0
diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf
index 5359caae38a..7133c13ae0c 100644
--- a/modules/nf-core/picard/sortvcf/main.nf
+++ b/modules/nf-core/picard/sortvcf/main.nf
@@ -4,8 +4,8 @@ process PICARD_SORTVCF {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' :
-        'biocontainers/picard:3.1.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' :
+        'biocontainers/picard:3.2.0--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(vcf)
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap
index e2e4a947cfa..8ff332c8b4a 100644
--- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap
@@ -2,15 +2,15 @@
     "homo_sapiens - cram": {
         "content": [
             "test.cram",
-            "test.cram.crai:md5,78d47ba01ac4e05f3ae1e353902a989e",
+            "test.cram.crai:md5,cb5268070f99cdd0d86f43613e5fc7db",
             "test.flagstat:md5,93b0ef463df947ede1f42ff60396c34d",
             "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15",
             "test.stats:md5,372a7d9d9081aa009b21343a913beb14",
             [
                 "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93",
                 "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1",
-                "versions.yml:md5,966dcea920866a87b55e665563864fc9",
                 "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656",
+                "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9",
                 "versions.yml:md5,fcf804c605f455127f2449403d70390c"
             ]
         ],
@@ -18,7 +18,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-03T11:55:09.400487"
+        "timestamp": "2024-07-10T09:50:25.483402093"
     },
     "sarscov2 - bam - stub": {
         "content": [
@@ -101,8 +101,8 @@
                 "9": [
                     "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93",
                     "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1",
-                    "versions.yml:md5,966dcea920866a87b55e665563864fc9",
                     "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656",
+                    "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9",
                     "versions.yml:md5,fcf804c605f455127f2449403d70390c"
                 ],
                 "bai": [
@@ -183,8 +183,8 @@
                 "versions": [
                     "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93",
                     "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1",
-                    "versions.yml:md5,966dcea920866a87b55e665563864fc9",
                     "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656",
+                    "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9",
                     "versions.yml:md5,fcf804c605f455127f2449403d70390c"
                 ]
             }
@@ -193,7 +193,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-03T11:55:22.514635"
+        "timestamp": "2024-07-10T09:50:45.745539171"
     },
     "homo_sapiens - cram - stub": {
         "content": [
@@ -268,8 +268,8 @@
                 "9": [
                     "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93",
                     "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1",
-                    "versions.yml:md5,966dcea920866a87b55e665563864fc9",
                     "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656",
+                    "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9",
                     "versions.yml:md5,fcf804c605f455127f2449403d70390c"
                 ],
                 "bai": [
@@ -342,8 +342,8 @@
                 "versions": [
                     "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93",
                     "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1",
-                    "versions.yml:md5,966dcea920866a87b55e665563864fc9",
                     "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656",
+                    "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9",
                     "versions.yml:md5,fcf804c605f455127f2449403d70390c"
                 ]
             }
@@ -352,20 +352,20 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-03T11:55:37.258086"
+        "timestamp": "2024-07-10T09:51:17.13987629"
     },
     "sarscov2 - bam": {
         "content": [
-            "test.bam:md5,3091fe6ba1b7530f382fe40b9fd8f45b",
-            "test.bam.bai:md5,4d3ae8d013444b55e17aa0149a2ab404",
+            "test.bam:md5,d1a53820e4a6e42ca8aceab51d74cf57",
+            "test.bam.bai:md5,be9485a644813773fb893a0a6b9b977c",
             "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783",
             "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2",
             "test.stats:md5,cca83e4fc9406fc3875b5e60055d6574",
             [
                 "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93",
                 "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1",
-                "versions.yml:md5,966dcea920866a87b55e665563864fc9",
                 "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656",
+                "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9",
                 "versions.yml:md5,fcf804c605f455127f2449403d70390c"
             ]
         ],
@@ -373,6 +373,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.2"
         },
-        "timestamp": "2024-07-03T11:54:53.226702"
+        "timestamp": "2024-07-10T09:50:01.597322113"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap
index 4e80c28cab4..f02de25e29c 100644
--- a/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap
@@ -57,15 +57,15 @@
                 "## htsjdk.samtools.metrics.StringHeader"
             ],
             [
-                "versions.yml:md5,d04aca83a6423efc7b818b0d3e0cb1ba",
-                "versions.yml:md5,e0ec5ed2685f50270d45602c891fad3b"
+                "versions.yml:md5,d61a29a9b3d8c60ed90b068df8032979",
+                "versions.yml:md5,e71b3af11ad159b26b503337cd90ee3d"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-06-07T10:41:38.304686"
+        "timestamp": "2024-07-10T09:38:29.298437201"
     },
     "sascov2_wgs - [bam,bai]": {
         "content": [
@@ -114,14 +114,14 @@
                 "## htsjdk.samtools.metrics.StringHeader"
             ],
             [
-                "versions.yml:md5,600deaee68c6f78bbdf023b794d7b4fe",
-                "versions.yml:md5,d04aca83a6423efc7b818b0d3e0cb1ba"
+                "versions.yml:md5,e71b3af11ad159b26b503337cd90ee3d",
+                "versions.yml:md5,ebe92bff64a6e7b1a0aa741674d24893"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2023-11-29T17:32:57.186833877"
+        "timestamp": "2024-07-10T09:38:09.338919835"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap b/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap
index 50341f650cc..993f58fd9ff 100644
--- a/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bcl_demultiplex/tests/main.nf.test.snap
@@ -24,7 +24,7 @@
                 ]
             ],
             [
-                "versions.yml:md5,a52db0d612f5a3f30d54194d9f7393cf"
+                "versions.yml:md5,bcf8fd3ee65f301e48280750fe2524d5"
             ],
             [
                 [
@@ -60,9 +60,9 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-05-07T09:13:44.123805878"
+        "timestamp": "2024-07-10T11:37:10.291289677"
     },
     "bcl2fastq": {
         "content": [
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 3672a771f06..53d6de82c75 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -70,9 +70,6 @@ bamutil/trimbam:
 bandage/image:
   - modules/nf-core/bandage/image/**
   - tests/modules/nf-core/bandage/image/**
-barrnap:
-  - modules/nf-core/barrnap/**
-  - tests/modules/nf-core/barrnap/**
 basicpy:
   - modules/nf-core/basicpy/**
   - tests/modules/nf-core/basicpy/**
@@ -103,9 +100,6 @@ bcftools/convert:
 bcftools/merge:
   - modules/nf-core/bcftools/merge/**
   - tests/modules/nf-core/bcftools/merge/**
-bcftools/pluginsplit:
-  - modules/nf-core/bcftools/pluginsplit/**
-  - tests/modules/nf-core/bcftools/pluginsplit/**
 bcftools/roh:
   - modules/nf-core/bcftools/roh/**
   - tests/modules/nf-core/bcftools/roh/**
@@ -869,18 +863,12 @@ lissero:
 lofreq/call:
   - modules/nf-core/lofreq/call/**
   - tests/modules/nf-core/lofreq/call/**
-lofreq/callparallel:
-  - modules/nf-core/lofreq/callparallel/**
-  - tests/modules/nf-core/lofreq/callparallel/**
 lofreq/filter:
   - modules/nf-core/lofreq/filter/**
   - tests/modules/nf-core/lofreq/filter/**
 lofreq/indelqual:
   - modules/nf-core/lofreq/indelqual/**
   - tests/modules/nf-core/lofreq/indelqual/**
-lofreq/somatic:
-  - modules/nf-core/lofreq/somatic/**
-  - tests/modules/nf-core/lofreq/somatic/**
 macrel/contigs:
   - modules/nf-core/macrel/contigs/**
   - tests/modules/nf-core/macrel/contigs/**
diff --git a/tests/modules/nf-core/barrnap/main.nf b/tests/modules/nf-core/barrnap/main.nf
deleted file mode 100644
index de58beedd71..00000000000
--- a/tests/modules/nf-core/barrnap/main.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BARRNAP } from '../../../../modules/nf-core/barrnap/main.nf'
-
-workflow test_barrnap {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
-    ]
-
-    BARRNAP ( input )
-}
diff --git a/tests/modules/nf-core/barrnap/nextflow.config b/tests/modules/nf-core/barrnap/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/barrnap/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/barrnap/test.yml b/tests/modules/nf-core/barrnap/test.yml
deleted file mode 100644
index 5586a72c8c9..00000000000
--- a/tests/modules/nf-core/barrnap/test.yml
+++ /dev/null
@@ -1,8 +0,0 @@
-- name: barrnap test_barrnap
-  command: nextflow run ./tests/modules/nf-core/barrnap -entry test_barrnap -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/barrnap/nextflow.config
-  tags:
-    - barrnap
-  files:
-    - path: output/barrnap/rrna_bac.gff
-      md5sum: df19e1b84ba6f691d20c72b397c88abf
-    - path: output/barrnap/versions.yml
diff --git a/tests/modules/nf-core/bcftools/pluginsplit/main.nf b/tests/modules/nf-core/bcftools/pluginsplit/main.nf
deleted file mode 100644
index abc615788d5..00000000000
--- a/tests/modules/nf-core/bcftools/pluginsplit/main.nf
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_PLUGINSPLIT } from '../../../../../modules/nf-core/bcftools/pluginsplit/main.nf'
-
-workflow test_bcftools_pluginsplit {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    samples = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
-        .collectFile(name:"samples.txt", newLine:true)
-
-    BCFTOOLS_PLUGINSPLIT (
-        input,
-        samples,
-        [],
-        [],
-        []
-    )
-}
-
-workflow test_bcftools_pluginsplit_full {
-    
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_tbi'], checkIfExists: true)
-    ]
-
-    groups = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
-        .collectFile(name:"samples.txt", newLine:true)
-
-    regions = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
-    targets = file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true)
-
-    BCFTOOLS_PLUGINSPLIT (
-        input,
-        [],
-        groups,
-        regions,
-        targets
-    )
-}
diff --git a/tests/modules/nf-core/bcftools/pluginsplit/nextflow.config b/tests/modules/nf-core/bcftools/pluginsplit/nextflow.config
deleted file mode 100644
index 50f50a7a357..00000000000
--- a/tests/modules/nf-core/bcftools/pluginsplit/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/bcftools/pluginsplit/test.yml b/tests/modules/nf-core/bcftools/pluginsplit/test.yml
deleted file mode 100644
index 48ecbfbff86..00000000000
--- a/tests/modules/nf-core/bcftools/pluginsplit/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: bcftools pluginsplit test_bcftools_pluginsplit
-  command: nextflow run ./tests/modules/nf-core/bcftools/pluginsplit -entry test_bcftools_pluginsplit -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/pluginsplit/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/pluginsplit
-  files:
-    - path: output/bcftools/normal.vcf
-      md5sum: 69cfc4bf92bf3e2847081a2026a4d3bb
-    - path: output/bcftools/tumour.vcf
-      md5sum: 08fa5c8d5561c2a8d7c300cb0eea1042
-    - path: output/bcftools/versions.yml
-
-- name: bcftools pluginsplit test_bcftools_pluginsplit_full
-  command: nextflow run ./tests/modules/nf-core/bcftools/pluginsplit -entry test_bcftools_pluginsplit_full -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bcftools/pluginsplit/nextflow.config
-  tags:
-    - bcftools
-    - bcftools/pluginsplit
-  files:
-    - path: output/bcftools/normal.vcf
-      md5sum: 78e962c3a724790b27041f28a4180600
-    - path: output/bcftools/tumour.vcf
-      md5sum: 3008a0a06a2f319897fa04ea0018fcdd
-    - path: output/bcftools/versions.yml
diff --git a/tests/modules/nf-core/lofreq/callparallel/main.nf b/tests/modules/nf-core/lofreq/callparallel/main.nf
deleted file mode 100644
index d37e439470f..00000000000
--- a/tests/modules/nf-core/lofreq/callparallel/main.nf
+++ /dev/null
@@ -1,33 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LOFREQ_CALLPARALLEL } from '../../../../../modules/nf-core/lofreq/callparallel/main.nf'
-
-workflow test_lofreq_callparallel {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-              []
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    LOFREQ_CALLPARALLEL ( input, fasta, fai )
-}
-
-workflow test_lofreq_callparallel_intervals {
-
-    input = [ [ id:'test' ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
-              file(params.test_data['sarscov2']['genome']['test_bed'])
-    ]
-
-    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-
-    LOFREQ_CALLPARALLEL ( input, fasta, fai )
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/lofreq/callparallel/nextflow.config b/tests/modules/nf-core/lofreq/callparallel/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/lofreq/callparallel/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
diff --git a/tests/modules/nf-core/lofreq/callparallel/test.yml b/tests/modules/nf-core/lofreq/callparallel/test.yml
deleted file mode 100644
index da3078f4406..00000000000
--- a/tests/modules/nf-core/lofreq/callparallel/test.yml
+++ /dev/null
@@ -1,23 +0,0 @@
-- name: lofreq callparallel test_lofreq_callparallel
-  command: nextflow run ./tests/modules/nf-core/lofreq/callparallel -entry test_lofreq_callparallel -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lofreq/callparallel/nextflow.config
-  tags:
-    - lofreq/callparallel
-    - lofreq
-  files:
-    - path: output/lofreq/test.vcf.gz
-      contains:
-        [
-          '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">',
-        ]
-
-- name: lofreq callparallel test_lofreq_callparallel_intervals
-  command: nextflow run ./tests/modules/nf-core/lofreq/callparallel -entry test_lofreq_callparallel_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lofreq/callparallel/nextflow.config
-  tags:
-    - lofreq/callparallel
-    - lofreq
-  files:
-    - path: output/lofreq/test.vcf.gz
-      contains:
-        [
-          '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">',
-        ]
diff --git a/tests/modules/nf-core/lofreq/somatic/main.nf b/tests/modules/nf-core/lofreq/somatic/main.nf
deleted file mode 100644
index b8a0e34a1d4..00000000000
--- a/tests/modules/nf-core/lofreq/somatic/main.nf
+++ /dev/null
@@ -1,28 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { LOFREQ_SOMATIC } from '../../../../../modules/nf-core/lofreq/somatic/main.nf'
-
-workflow test_lofreq_somatic {
-
-    input = [
-        [ id:'test_', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
-        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-    ]
-
-    fasta = [
-        [id:'test_genome'],
-        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
-    ]
-    fai = [
-        [id:'test_genome_index'],
-        file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
-    ]
-
-    LOFREQ_SOMATIC ( input, fasta, fai )
-}
diff --git a/tests/modules/nf-core/lofreq/somatic/nextflow.config b/tests/modules/nf-core/lofreq/somatic/nextflow.config
deleted file mode 100644
index 19934e76a97..00000000000
--- a/tests/modules/nf-core/lofreq/somatic/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-}
\ No newline at end of file
diff --git a/tests/modules/nf-core/lofreq/somatic/test.yml b/tests/modules/nf-core/lofreq/somatic/test.yml
deleted file mode 100644
index 5d53aed992d..00000000000
--- a/tests/modules/nf-core/lofreq/somatic/test.yml
+++ /dev/null
@@ -1,37 +0,0 @@
-- name: lofreq somatic test_lofreq_somatic
-  command: nextflow run ./tests/modules/nf-core/lofreq/somatic -entry test_lofreq_somatic -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/lofreq/somatic/nextflow.config
-  tags:
-    - lofreq/somatic
-    - lofreq
-  files:
-    - path: output/lofreq/test_normal_relaxed.vcf.gz
-      contains:
-        - '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">'
-    - path: output/lofreq/test_normal_stringent.indels.vcf.gz
-      contains:
-        - '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">'
-    - path: output/lofreq/test_normal_stringent.snvs.vcf.gz
-      contains:
-        - '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">'
-    - path: output/lofreq/test_somatic_final.indels.vcf.gz
-      contains:
-        - '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">'
-    - path: output/lofreq/test_somatic_final.snvs.vcf.gz
-      contains:
-        - '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">'
-    - path: output/lofreq/test_somatic_raw.indels.vcf.gz
-      contains:
-        - '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">'
-    - path: output/lofreq/test_somatic_raw.snvs.vcf.gz
-      contains:
-        - '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">'
-    - path: output/lofreq/test_tumor_relaxed.vcf.gz
-      contains:
-        - '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">'
-    - path: output/lofreq/test_tumor_stringent.indels.vcf.gz
-      contains:
-        - '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">'
-    - path: output/lofreq/test_tumor_stringent.snvs.vcf.gz
-      contains:
-        - '##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">'
-    - path: output/lofreq/versions.yml