From 03a9f356a1a333923c1177c2912fa7bc61bb46f3 Mon Sep 17 00:00:00 2001
From: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
Date: Thu, 14 Nov 2024 13:51:04 +0200
Subject: [PATCH 01/12] =?UTF-8?q?hmmalign=20ported=20to=20nf-test,=20versi?=
 =?UTF-8?q?on=20bump,=20wave=20container,=20standard=20ou=E2=80=A6=20(#699?=
 =?UTF-8?q?2)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

hmmalign ported to nf-test, version bump, wave container, standard output format, hmmbuild version bump, wave container, subworkflow updated accordingly
---
 .../nf-core/hmmer/hmmalign/environment.yml    |   2 +-
 modules/nf-core/hmmer/hmmalign/main.nf        |  21 ++-
 modules/nf-core/hmmer/hmmalign/meta.yml       |   7 +-
 .../nf-core/hmmer/hmmalign/tests/main.nf.test |  58 +++++++
 .../hmmer/hmmalign/tests/main.nf.test.snap    |  68 ++++++++
 .../nf-core/hmmer/hmmbuild/environment.yml    |   2 +-
 modules/nf-core/hmmer/hmmbuild/main.nf        |   4 +-
 .../nf-core/hmmer/hmmbuild/tests/main.nf.test |  12 +-
 .../hmmer/hmmbuild/tests/main.nf.test.snap    |  14 +-
 .../nf-core/fasta_newick_epang_gappa/main.nf  |   4 +-
 .../tests/main.nf.test.snap                   | 164 +++++++++---------
 tests/config/pytest_modules.yml               |   3 -
 tests/modules/nf-core/hmmer/hmmalign/main.nf  |  30 ----
 .../nf-core/hmmer/hmmalign/nextflow.config    |   8 -
 tests/modules/nf-core/hmmer/hmmalign/test.yml |  16 --
 15 files changed, 247 insertions(+), 166 deletions(-)
 create mode 100644 modules/nf-core/hmmer/hmmalign/tests/main.nf.test
 create mode 100644 modules/nf-core/hmmer/hmmalign/tests/main.nf.test.snap
 delete mode 100644 tests/modules/nf-core/hmmer/hmmalign/main.nf
 delete mode 100644 tests/modules/nf-core/hmmer/hmmalign/nextflow.config
 delete mode 100644 tests/modules/nf-core/hmmer/hmmalign/test.yml

diff --git a/modules/nf-core/hmmer/hmmalign/environment.yml b/modules/nf-core/hmmer/hmmalign/environment.yml
index 7c62eac7e3a..c5ddec5d912 100644
--- a/modules/nf-core/hmmer/hmmalign/environment.yml
+++ b/modules/nf-core/hmmer/hmmalign/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::hmmer=3.3.2
+  - bioconda::hmmer=3.4
diff --git a/modules/nf-core/hmmer/hmmalign/main.nf b/modules/nf-core/hmmer/hmmalign/main.nf
index 00ae8da2b95..39b17c787d8 100644
--- a/modules/nf-core/hmmer/hmmalign/main.nf
+++ b/modules/nf-core/hmmer/hmmalign/main.nf
@@ -4,16 +4,16 @@ process HMMER_HMMALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h1b792b2_1' :
-        'biocontainers/hmmer:3.3.2--h1b792b2_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/07/07c4cbd91c4459dc86b13b5cd799cacba96b27d66c276485550d299c7a4c6f8a/data' :
+        'community.wave.seqera.io/library/hmmer:3.4--cb5d2dd2e85974ca' }"
 
     input:
     tuple val(meta), path(fasta)
     path hmm
 
     output:
-    tuple val(meta), path("*.sthlm.gz"), emit: sthlm
-    path "versions.yml"                , emit: versions
+    tuple val(meta), path("*.sto.gz"), emit: sto
+    path "versions.yml"              , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,7 +25,18 @@ process HMMER_HMMALIGN {
     hmmalign \\
         $args \\
         $hmm \\
-        $fasta | gzip -c > ${prefix}.sthlm.gz
+        $fasta | gzip -c > ${prefix}.sto.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hmmer: \$(hmmalign -h | grep -o '^# HMMER [0-9.]*' | sed 's/^# HMMER *//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo | gzip > ${prefix}.sto.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/hmmer/hmmalign/meta.yml b/modules/nf-core/hmmer/hmmalign/meta.yml
index 366cf4f5a58..fb16ba6822e 100644
--- a/modules/nf-core/hmmer/hmmalign/meta.yml
+++ b/modules/nf-core/hmmer/hmmalign/meta.yml
@@ -30,16 +30,16 @@ input:
         description: A gzipped HMM file
         pattern: "*.hmm.gz"
 output:
-  - sthlm:
+  - sto:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.sthlm.gz":
+      - "*.sto.gz":
           type: file
           description: Multiple alignment in gzipped Stockholm format
-          pattern: "*.sthlm.gz"
+          pattern: "*.sto.gz"
   - versions:
       - versions.yml:
           type: file
@@ -51,3 +51,4 @@ authors:
 maintainers:
   - "@erikrikarddaniel"
   - "@jfy133"
+  - "@vagkaratzas"
diff --git a/modules/nf-core/hmmer/hmmalign/tests/main.nf.test b/modules/nf-core/hmmer/hmmalign/tests/main.nf.test
new file mode 100644
index 00000000000..7b0368fc630
--- /dev/null
+++ b/modules/nf-core/hmmer/hmmalign/tests/main.nf.test
@@ -0,0 +1,58 @@
+
+nextflow_process {
+
+    name "Test Process HMMER_HMMALIGN"
+    script "../main.nf"
+    process "HMMER_HMMALIGN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "hmmer"
+    tag "hmmer/hmmalign"
+
+    test("test-hmmer-hmmalign") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'delete_me/hmmer/e_coli_k12_16s.fna.gz', checkIfExists: true)
+                ]
+				input[1] = file(params.modules_testdata_base_path + 'delete_me/hmmer/bac.16S_rRNA.hmm.gz', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-hmmer-hmmalign-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id: 'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'delete_me/hmmer/e_coli_k12_16s.fna.gz', checkIfExists: true)
+                ]
+				input[1] = file(params.modules_testdata_base_path + 'delete_me/hmmer/bac.16S_rRNA.hmm.gz', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/hmmer/hmmalign/tests/main.nf.test.snap b/modules/nf-core/hmmer/hmmalign/tests/main.nf.test.snap
new file mode 100644
index 00000000000..ae65cacb18b
--- /dev/null
+++ b/modules/nf-core/hmmer/hmmalign/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "test-hmmer-hmmalign": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.sto.gz:md5,4ae989d5ade2aaae9578cb88ba031e8f"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,601e13e7a1e6057766d862a828d501c4"
+                ],
+                "sto": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.sto.gz:md5,4ae989d5ade2aaae9578cb88ba031e8f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,601e13e7a1e6057766d862a828d501c4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
+        },
+        "timestamp": "2024-11-13T12:37:26.551497424"
+    },
+    "test-hmmer-hmmalign-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.sto.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,601e13e7a1e6057766d862a828d501c4"
+                ],
+                "sto": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.sto.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,601e13e7a1e6057766d862a828d501c4"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
+        },
+        "timestamp": "2024-11-13T12:37:32.244343836"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/hmmer/hmmbuild/environment.yml b/modules/nf-core/hmmer/hmmbuild/environment.yml
index 7c62eac7e3a..c5ddec5d912 100644
--- a/modules/nf-core/hmmer/hmmbuild/environment.yml
+++ b/modules/nf-core/hmmer/hmmbuild/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::hmmer=3.3.2
+  - bioconda::hmmer=3.4
diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf
index b4629cb47a6..8eed7fcd7ad 100644
--- a/modules/nf-core/hmmer/hmmbuild/main.nf
+++ b/modules/nf-core/hmmer/hmmbuild/main.nf
@@ -4,8 +4,8 @@ process HMMER_HMMBUILD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hmmer:3.3.2--h87f3376_2':
-        'biocontainers/hmmer:3.3.2--h1b792b2_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/07/07c4cbd91c4459dc86b13b5cd799cacba96b27d66c276485550d299c7a4c6f8a/data' :
+        'community.wave.seqera.io/library/hmmer:3.4--cb5d2dd2e85974ca' }"
 
     input:
     tuple val(meta), path(alignment)
diff --git a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test
index d7c058255ea..635f5b661f1 100644
--- a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test
+++ b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test
@@ -16,9 +16,9 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-				    [ id: 'PF14720' ], // meta map
-				    file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true)
-				]
+                                [ id: 'PF14720' ], // meta map
+                                file(params.modules_testdata_base_path + 'delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true)
+                            ]
 				input[1] = []
 
                 """
@@ -46,9 +46,9 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-				    [ id: 'PF14720' ], // meta map
-				    file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true)
-				]
+                                [ id: 'PF14720' ], // meta map
+                                file(params.modules_testdata_base_path + 'delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true)
+                            ]
 				input[1] = []
 
                 """
diff --git a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap
index 8cdff17c142..79317b89ebd 100644
--- a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap
+++ b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap
@@ -14,7 +14,7 @@
                     "PF14720.hmmbuild.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "2": [
-                    "versions.yml:md5,6f4796b714cb0d5981cd12d9e89cb599"
+                    "versions.yml:md5,f8a0bffcbbc58404752849403812905b"
                 ],
                 "hmm": [
                     [
@@ -28,28 +28,28 @@
                     "PF14720.hmmbuild.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "versions": [
-                    "versions.yml:md5,6f4796b714cb0d5981cd12d9e89cb599"
+                    "versions.yml:md5,f8a0bffcbbc58404752849403812905b"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-09-05T21:38:44.751216"
+        "timestamp": "2024-11-13T12:52:29.794123574"
     },
     "test-hmmer-hmmbuild": {
         "content": [
             "PF14720.hmm.gz",
             "PF14720.hmmbuild.txt",
             [
-                "versions.yml:md5,6f4796b714cb0d5981cd12d9e89cb599"
+                "versions.yml:md5,f8a0bffcbbc58404752849403812905b"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-09-05T21:49:25.772308"
+        "timestamp": "2024-11-13T12:52:23.95935055"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/fasta_newick_epang_gappa/main.nf b/subworkflows/nf-core/fasta_newick_epang_gappa/main.nf
index 28016014f94..723f4a2d91a 100644
--- a/subworkflows/nf-core/fasta_newick_epang_gappa/main.nf
+++ b/subworkflows/nf-core/fasta_newick_epang_gappa/main.nf
@@ -82,10 +82,10 @@ workflow FASTA_NEWICK_EPANG_GAPPA {
     ch_versions = ch_versions.mix(HMMER_HMMALIGNQUERY.out.versions)
 
     // 1.d Mask the alignments (Add '--rf-is-mask' ext.args in config for the process.)
-    HMMER_MASKREF ( HMMER_HMMALIGNREF.out.sthlm.map { [ it[0], it[1], [], [], [], [], [], [] ] }, [] )
+    HMMER_MASKREF ( HMMER_HMMALIGNREF.out.sto.map { [ it[0], it[1], [], [], [], [], [], [] ] }, [] )
     ch_versions = ch_versions.mix(HMMER_MASKREF.out.versions)
 
-    HMMER_MASKQUERY ( HMMER_HMMALIGNQUERY.out.sthlm.map { [ it[0], it[1], [], [], [], [], [], [] ] }, [] )
+    HMMER_MASKQUERY ( HMMER_HMMALIGNQUERY.out.sto.map { [ it[0], it[1], [], [], [], [], [], [] ] }, [] )
     ch_versions = ch_versions.mix(HMMER_MASKQUERY.out.versions)
 
     // 1.e Reformat alignments to "afa" (aligned fasta)
diff --git a/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test.snap
index e6627edbe99..207d28e5013 100644
--- a/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fasta_newick_epang_gappa/tests/main.nf.test.snap
@@ -4,201 +4,201 @@
             "hmmer.taxonomy.per_query.tsv"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-05T20:45:46.123551197"
+        "timestamp": "2024-11-14T10:16:44.874521222"
     },
     "mafft.taxonomy.profile.tsv_lines": {
         "content": "eb4ae24c330c4b4ab768f7d1c26c7215",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T11:24:06.138041"
+        "timestamp": "2024-11-14T10:16:59.978336429"
+    },
+    "hmmer.graft.placement.epa_result.newick_lines": {
+        "content": "8533b159d543f75b92efcfb4fd330280",
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
+        },
+        "timestamp": "2024-11-14T10:16:44.866852673"
     },
     "hmmer.taxonomy.profile.tsv": {
         "content": [
             "hmmer.taxonomy.profile.tsv"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-05T20:45:46.115530176"
-    },
-    "hmmer.graft.placement.epa_result.newick_lines": {
-        "content": "8533b159d543f75b92efcfb4fd330280",
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T10:55:06.361779"
+        "timestamp": "2024-11-14T10:16:44.868720482"
     },
     "hmmer.taxonomy.profile.tsv_lines": {
         "content": "8533b159d543f75b92efcfb4fd330280",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T10:59:31.223864"
+        "timestamp": "2024-11-14T10:16:44.871385161"
     },
     "mafft.graft.placement.epa_result.newick_lines": {
         "content": "eb4ae24c330c4b4ab768f7d1c26c7215",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T11:24:06.117996"
+        "timestamp": "2024-11-14T10:16:59.973967772"
     },
     "mafft.taxonomy.per_query.tsv_lines": {
         "content": "eb4ae24c330c4b4ab768f7d1c26c7215",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T11:24:06.175662"
+        "timestamp": "2024-11-14T10:16:59.98411855"
     },
     "nucl_hmmer.versions.yml": {
         "content": [
             "versions.yml"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T13:37:42.212896"
+        "timestamp": "2024-11-14T10:17:41.730837855"
     },
     "hmmer.graft.placement.epa_result.newick": {
         "content": [
             "hmmer.graft.hmmer.epa_result.newick"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-05T20:45:46.105219765"
+        "timestamp": "2024-11-14T10:16:44.863462591"
     },
     "hmmer.versions.yml": {
         "content": [
             "versions.yml"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T13:37:05.782093"
+        "timestamp": "2024-11-14T10:16:44.880743216"
     },
-    "nucl_hmmer.graft.placement.epa_result.newick": {
+    "hmmer.epa_result.jplace.gz": {
         "content": [
-            "nucl_hmmer.graft.nucl_hmmer.epa_result.newick"
+            "hmmer.epa_result.jplace.gz"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T11:37:46.19414"
+        "timestamp": "2024-11-14T10:16:44.857734455"
     },
-    "hmmer.epa_result.jplace.gz": {
+    "nucl_hmmer.graft.placement.epa_result.newick": {
         "content": [
-            "hmmer.epa_result.jplace.gz"
+            "nucl_hmmer.graft.nucl_hmmer.epa_result.newick"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T11:56:49.564967"
+        "timestamp": "2024-11-14T10:17:41.728034651"
     },
     "hmmer.taxonomy.per_query.tsv_lines": {
         "content": "8533b159d543f75b92efcfb4fd330280",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T10:59:31.236689"
+        "timestamp": "2024-11-14T10:16:44.878231148"
     },
     "mafft.taxonomy.per_query.tsv": {
         "content": [
             "mafft.taxonomy.per_query.tsv"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-05T20:57:13.505168194"
+        "timestamp": "2024-11-14T10:16:59.980370338"
     },
     "mafft.graft.placement.epa_result.newick": {
         "content": [
             "mafft.graft.mafft.epa_result.newick"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-05T20:57:13.49856233"
+        "timestamp": "2024-11-14T10:16:59.972095017"
     },
     "nucl_hmmer.epa_result.jplace.gz": {
         "content": [
             "nucl_hmmer.epa_result.jplace.gz"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T11:44:49.494246"
+        "timestamp": "2024-11-14T10:17:41.725684052"
     },
     "nucl_hmmer.versions.yml_lines": {
-        "content": "664dc00d47aecd41a420dc6ba7ef4eea",
+        "content": "eafb4184937621216ff03df17c4245a6",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T13:37:42.217138"
+        "timestamp": "2024-11-14T10:17:41.733022413"
     },
-    "mafft.taxonomy.profile.tsv": {
-        "content": [
-            "mafft.taxonomy.profile.tsv"
-        ],
+    "hmmer.versions.yml_lines": {
+        "content": "eafb4184937621216ff03df17c4245a6",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-05T20:57:13.501534227"
+        "timestamp": "2024-11-14T10:16:44.884598465"
     },
     "mafft.epa_result.jplace.gz": {
         "content": [
             "mafft.epa_result.jplace.gz"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T11:57:06.815658"
+        "timestamp": "2024-11-14T10:16:59.970209461"
     },
-    "hmmer.versions.yml_lines": {
-        "content": "664dc00d47aecd41a420dc6ba7ef4eea",
+    "mafft.taxonomy.profile.tsv": {
+        "content": [
+            "mafft.taxonomy.profile.tsv"
+        ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T13:37:05.849215"
+        "timestamp": "2024-11-14T10:16:59.975738553"
     },
     "mafft.versions.yml": {
         "content": [
             "versions.yml"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T13:37:20.88609"
+        "timestamp": "2024-11-14T10:16:59.986610634"
     },
     "mafft.versions.yml_lines": {
         "content": "f5957093def0191f32bb294000fb9242",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
         },
-        "timestamp": "2024-04-08T13:37:20.890963"
+        "timestamp": "2024-11-14T10:16:59.988948939"
     }
 }
\ No newline at end of file
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 55984e2de9e..2e0e6420c33 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -299,9 +299,6 @@ hmmer/eslalimask:
 hmmer/eslreformat:
   - modules/nf-core/hmmer/eslreformat/**
   - tests/modules/nf-core/hmmer/eslreformat/**
-hmmer/hmmalign:
-  - modules/nf-core/hmmer/hmmalign/**
-  - tests/modules/nf-core/hmmer/hmmalign/**
 hmtnote/annotate:
   - modules/nf-core/hmtnote/annotate/**
   - tests/modules/nf-core/hmtnote/annotate/**
diff --git a/tests/modules/nf-core/hmmer/hmmalign/main.nf b/tests/modules/nf-core/hmmer/hmmalign/main.nf
deleted file mode 100644
index 64814641c3d..00000000000
--- a/tests/modules/nf-core/hmmer/hmmalign/main.nf
+++ /dev/null
@@ -1,30 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { HMMER_HMMALIGN as HMMER_HMMALIGN        } from '../../../../../modules/nf-core/hmmer/hmmalign/main.nf'
-include { HMMER_HMMALIGN as HMMER_HMMALIGN_PREFIX } from '../../../../../modules/nf-core/hmmer/hmmalign/main.nf'
-
-workflow test_hmmer_hmmalign {
-
-    input = [
-        [ id:'test' ], // meta map
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config
-    ]
-
-    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
-
-    HMMER_HMMALIGN ( input, hmm )
-}
-
-workflow test_hmmer_hmmalign_prefix {
-
-    input = [
-        [ id:'test' ], // meta map
-        file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/e_coli_k12_16s.fna.gz')      // Change to params.test_data syntax after the data is included in ./tests/config/test_data.config
-    ]
-
-    hmm   = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/hmmer/bac.16S_rRNA.hmm.gz')
-
-    HMMER_HMMALIGN_PREFIX ( input, hmm )
-}
diff --git a/tests/modules/nf-core/hmmer/hmmalign/nextflow.config b/tests/modules/nf-core/hmmer/hmmalign/nextflow.config
deleted file mode 100644
index b2115af55d9..00000000000
--- a/tests/modules/nf-core/hmmer/hmmalign/nextflow.config
+++ /dev/null
@@ -1,8 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: HMMER_HMMALIGN_PREFIX {
-        ext.prefix = { "${meta.id}.prefix" }
-    }
-}
diff --git a/tests/modules/nf-core/hmmer/hmmalign/test.yml b/tests/modules/nf-core/hmmer/hmmalign/test.yml
deleted file mode 100644
index 2f483956c98..00000000000
--- a/tests/modules/nf-core/hmmer/hmmalign/test.yml
+++ /dev/null
@@ -1,16 +0,0 @@
-- name: hmmer hmmalign test_hmmer_hmmalign
-  command: nextflow run ./tests/modules/nf-core/hmmer/hmmalign -entry test_hmmer_hmmalign -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hmmer/hmmalign/nextflow.config
-  tags:
-    - hmmer
-    - hmmer/hmmalign
-  files:
-    - path: output/hmmer/test.sthlm.gz
-      md5sum: ddaa8b96291edf4e1a929a224329161b
-- name: hmmer hmmalign test_hmmer_hmmalign_prefix
-  command: nextflow run ./tests/modules/nf-core/hmmer/hmmalign -entry test_hmmer_hmmalign_prefix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hmmer/hmmalign/nextflow.config
-  tags:
-    - hmmer
-    - hmmer/hmmalign
-  files:
-    - path: output/hmmer/test.prefix.sthlm.gz
-      md5sum: ddaa8b96291edf4e1a929a224329161b

From 920895254d42e874c035d07d783d40da7395c2da Mon Sep 17 00:00:00 2001
From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Date: Thu, 14 Nov 2024 18:12:33 +0530
Subject: [PATCH 02/12] Fix/biscuit apps (#6979)

* init update biscuit apps

* update index module + test; use seqera container

* update align module + test; use seqera container

* update blaster container + test

* update container + test

* update container + test

* update mergecg container + test + rm tags.yml

* update pileup container + test

* update index container

* update qc container + test

* update vcf2bed container + test

* fix biscuit, samtools cpu determination
---
 modules/nf-core/biscuit/align/environment.yml |   4 +-
 modules/nf-core/biscuit/align/main.nf         |  33 ++++--
 modules/nf-core/biscuit/align/meta.yml        |  21 +++-
 .../nf-core/biscuit/align/tests/main.nf.test  |  70 ++++++++++--
 .../biscuit/align/tests/main.nf.test.snap     |  87 ++++++++++++--
 modules/nf-core/biscuit/align/tests/tags.yml  |   3 -
 .../biscuit/biscuitblaster/environment.yml    |   4 +-
 .../nf-core/biscuit/biscuitblaster/main.nf    |  32 +++---
 .../nf-core/biscuit/biscuitblaster/meta.yml   |  24 +++-
 .../biscuit/biscuitblaster/tests/main.nf.test |  58 ++++++----
 .../biscuitblaster/tests/main.nf.test.snap    |  53 ++++-----
 .../biscuit/biscuitblaster/tests/tags.yml     |   2 -
 .../nf-core/biscuit/bsconv/environment.yml    |   2 +-
 modules/nf-core/biscuit/bsconv/main.nf        |  19 ++-
 modules/nf-core/biscuit/bsconv/meta.yml       |  26 ++++-
 .../nf-core/biscuit/bsconv/tests/main.nf.test |  49 +++++---
 .../biscuit/bsconv/tests/main.nf.test.snap    |  63 ++--------
 modules/nf-core/biscuit/bsconv/tests/tags.yml |   2 -
 .../nf-core/biscuit/epiread/environment.yml   |   4 +-
 modules/nf-core/biscuit/epiread/main.nf       |  31 +++--
 modules/nf-core/biscuit/epiread/meta.yml      |  35 +++++-
 .../biscuit/epiread/tests/main.nf.test        |  92 +++++++++++----
 .../biscuit/epiread/tests/main.nf.test.snap   |  92 +++++++--------
 modules/nf-core/biscuit/index/environment.yml |   2 +-
 modules/nf-core/biscuit/index/main.nf         |  11 +-
 modules/nf-core/biscuit/index/meta.yml        |  18 ++-
 .../nf-core/biscuit/index/tests/main.nf.test  |  17 +--
 .../biscuit/index/tests/main.nf.test.snap     | 108 +++++++++++-------
 .../nf-core/biscuit/mergecg/environment.yml   |   4 +-
 modules/nf-core/biscuit/mergecg/main.nf       |  21 ++--
 modules/nf-core/biscuit/mergecg/meta.yml      |  21 +++-
 .../biscuit/mergecg/tests/main.nf.test        |  47 ++++----
 .../biscuit/mergecg/tests/main.nf.test.snap   |  36 +++---
 .../nf-core/biscuit/mergecg/tests/tags.yml    |   2 -
 .../nf-core/biscuit/pileup/environment.yml    |   4 +-
 modules/nf-core/biscuit/pileup/main.nf        |  15 +--
 modules/nf-core/biscuit/pileup/meta.yml       |  19 ++-
 .../nf-core/biscuit/pileup/tests/main.nf.test |  36 ++++--
 .../biscuit/pileup/tests/main.nf.test.snap    |  64 +++++------
 modules/nf-core/biscuit/qc/environment.yml    |   2 +-
 modules/nf-core/biscuit/qc/main.nf            |  13 ++-
 modules/nf-core/biscuit/qc/meta.yml           |  20 +++-
 modules/nf-core/biscuit/qc/tests/main.nf.test |  21 +++-
 .../biscuit/qc/tests/main.nf.test.snap        |  28 ++---
 .../nf-core/biscuit/vcf2bed/environment.yml   |   4 +-
 modules/nf-core/biscuit/vcf2bed/main.nf       |  12 +-
 modules/nf-core/biscuit/vcf2bed/meta.yml      |   1 +
 .../biscuit/vcf2bed/tests/main.nf.test        |  14 +--
 .../biscuit/vcf2bed/tests/main.nf.test.snap   |  24 ++--
 49 files changed, 839 insertions(+), 531 deletions(-)
 delete mode 100644 modules/nf-core/biscuit/align/tests/tags.yml
 delete mode 100644 modules/nf-core/biscuit/biscuitblaster/tests/tags.yml
 delete mode 100644 modules/nf-core/biscuit/bsconv/tests/tags.yml
 delete mode 100644 modules/nf-core/biscuit/mergecg/tests/tags.yml

diff --git a/modules/nf-core/biscuit/align/environment.yml b/modules/nf-core/biscuit/align/environment.yml
index b4bab59944c..222c156ed9a 100644
--- a/modules/nf-core/biscuit/align/environment.yml
+++ b/modules/nf-core/biscuit/align/environment.yml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::biscuit=1.1.0.20220707
-  - bioconda::samtools=1.16.1
+  - bioconda::biscuit=1.5.0.20240506
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/biscuit/align/main.nf b/modules/nf-core/biscuit/align/main.nf
index 5154748725d..0d43dc05183 100644
--- a/modules/nf-core/biscuit/align/main.nf
+++ b/modules/nf-core/biscuit/align/main.nf
@@ -4,12 +4,13 @@ process BISCUIT_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-d94f582b04a3edcede1215189c0d881506640fd9:6519548ea4f3d6a526c78ad0350c58f867f28574-0':
-        'biocontainers/mulled-v2-d94f582b04a3edcede1215189c0d881506640fd9:6519548ea4f3d6a526c78ad0350c58f867f28574-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5b/5b542bbe1f99afd494ef07423ea8b52f2b8a081b85f92db2726c283c78da3cf0/data':
+        'community.wave.seqera.io/library/biscuit_samtools:84373c8a97fa63b8' }"
 
     input:
     tuple val(meta), path(reads)
-    path index
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(index)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -23,18 +24,34 @@ process BISCUIT_ALIGN {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def biscuit_cpus = (int) Math.max(Math.floor(task.cpus*0.9),1)
-    def samtools_cpus = task.cpus-biscuit_cpus
+    def biscuit_cpus = [(task.cpus * 0.9) as int, 1].max()
+    def samtools_cpus = (task.cpus - biscuit_cpus < 1) ? biscuit_cpus : (task.cpus - biscuit_cpus)
     """
-    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/\\.bis.amb\$//'`
+    ln -sf \$(readlink $fasta) $index/$fasta
 
     biscuit align \\
         $args \\
         -@ $biscuit_cpus \\
-        \$INDEX \\
+        $index/$fasta \\
         $reads \\
-        | samtools sort $args2 --threads $samtools_cpus --write-index -o ${prefix}.bam##idx##${prefix}.bam.bai -
+        | samtools sort $args2 --threads $samtools_cpus --write-index -o ${prefix}.bam -O BAM -
 
+    samtools index ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        biscuit: \$( biscuit version |& sed '1!d; s/^.*BISCUIT Version: //' )
+        samtools: \$( samtools --version |& sed '1!d; s/^.*samtools //' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+    touch ${prefix}.bam.bai
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/biscuit/align/meta.yml b/modules/nf-core/biscuit/align/meta.yml
index 645fc2c98a3..464e435bfa9 100644
--- a/modules/nf-core/biscuit/align/meta.yml
+++ b/modules/nf-core/biscuit/align/meta.yml
@@ -27,12 +27,24 @@ input:
     - reads:
         type: file
         description: |
-          List of input fastq files of size 1 and 2 for single-end and paired-end data,
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
-  - - index:
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - index:
         type: directory
-        description: Biscuit genome index directory (generated with 'biscuit index')
-        pattern: "BiscuitIndex"
+        description: Directory containing biscuit genome index
 output:
   - bam:
       - meta:
@@ -63,3 +75,4 @@ authors:
   - "@njspix"
 maintainers:
   - "@njspix"
+  - "@sateeshperi"
diff --git a/modules/nf-core/biscuit/align/tests/main.nf.test b/modules/nf-core/biscuit/align/tests/main.nf.test
index 1dc3eb3faca..84feb7a2249 100644
--- a/modules/nf-core/biscuit/align/tests/main.nf.test
+++ b/modules/nf-core/biscuit/align/tests/main.nf.test
@@ -12,16 +12,19 @@ nextflow_process {
 
     setup {
         run("BISCUIT_INDEX") {
-            script "../../index/main.nf"
+            script "../../../biscuit/index/main.nf"
             process {
             """
-            input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+            input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+            ])
             """
         }
         }
     }
 
-    test("Single-End sarscov2 test_methylated_1 [fastq_gz]") {
+    test("sarscov2 single-end [fastq_gz]") {
 
         when {
             process {
@@ -30,7 +33,11 @@ nextflow_process {
                             [ id:'test' ], // meta map
                             [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) ]
                 ]
-                input[1] = BISCUIT_INDEX.out.index
+                input[1] = Channel.of([
+                                [ id:'test' ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -38,14 +45,17 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert file(process.out.bam[0][1]).name == "test.bam" },
-                { assert file(process.out.bai[0][1]).name == "test.bam.bai" },
-                { assert snapshot(process.out.versions).match("single-end-versions") }
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+                    process.out.bai,
+					process.out.versions
+					).match()
+				}
           )
         }
     }
 
-    test("Paired-End sarscov2 test_methylated_1 [fastq_gz]") {
+    test("sarscov2 paired-end [fastq_gz]") {
 
         when {
             process {
@@ -55,7 +65,11 @@ nextflow_process {
                             [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true),
                               file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) ]
                 ]
-                input[1] = BISCUIT_INDEX.out.index
+                input[1] = Channel.of([
+                                [ id:'test' ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -63,9 +77,41 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert file(process.out.bam[0][1]).name == "test.bam" },
-                { assert file(process.out.bai[0][1]).name == "test.bam.bai" },
-                { assert snapshot(process.out.versions).match("paired-end-versions") }
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+                    process.out.bai,
+					process.out.versions
+					).match()
+				}
+          )
+        }
+    }
+
+    test("sarscov2 paired-end [fastq_gz] - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test' ], // meta map
+                            [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true),
+                              file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) ]
+                ]
+                input[1] = Channel.of([
+                                [ id:'test' ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match()
+				}
           )
         }
     }
diff --git a/modules/nf-core/biscuit/align/tests/main.nf.test.snap b/modules/nf-core/biscuit/align/tests/main.nf.test.snap
index 5776f87c62f..b6aeda38f7b 100644
--- a/modules/nf-core/biscuit/align/tests/main.nf.test.snap
+++ b/modules/nf-core/biscuit/align/tests/main.nf.test.snap
@@ -1,26 +1,93 @@
 {
-    "single-end-versions": {
+    "sarscov2 single-end [fastq_gz]": {
         "content": [
+            "499055250804bb3674c724bd9adf9d02",
             [
-                "versions.yml:md5,0b2a8c4c438a785a890110a458399bfd"
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bam.bai:md5,a748afc3cec6c27906ae80638e2024f5"
+                ]
+            ],
+            [
+                "versions.yml:md5,18c276eafa69dc43fa4d5b83b8392016"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-22T20:06:02.295706212"
+        "timestamp": "2024-11-14T10:03:51.461022384"
     },
-    "paired-end-versions": {
+    "sarscov2 paired-end [fastq_gz]": {
         "content": [
+            "6b5afc62da5533472e1479950bb5f09a",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bam.bai:md5,ba60b802f583496e330c555bca9f0b97"
+                ]
+            ],
             [
-                "versions.yml:md5,0b2a8c4c438a785a890110a458399bfd"
+                "versions.yml:md5,18c276eafa69dc43fa4d5b83b8392016"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T10:04:02.88266119"
+    },
+    "sarscov2 paired-end [fastq_gz] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,18c276eafa69dc43fa4d5b83b8392016"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,18c276eafa69dc43fa4d5b83b8392016"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-22T20:06:17.879689395"
+        "timestamp": "2024-11-13T06:48:19.558887499"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/biscuit/align/tests/tags.yml b/modules/nf-core/biscuit/align/tests/tags.yml
deleted file mode 100644
index d73b8183f7f..00000000000
--- a/modules/nf-core/biscuit/align/tests/tags.yml
+++ /dev/null
@@ -1,3 +0,0 @@
-biscuit/align:
-  - modules/nf-core/biscuit/index/**
-  - modules/nf-core/biscuit/align/**
diff --git a/modules/nf-core/biscuit/biscuitblaster/environment.yml b/modules/nf-core/biscuit/biscuitblaster/environment.yml
index ba50e31d11c..74a7b2fb908 100644
--- a/modules/nf-core/biscuit/biscuitblaster/environment.yml
+++ b/modules/nf-core/biscuit/biscuitblaster/environment.yml
@@ -2,6 +2,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::biscuit=1.1.0.20220707
+  - bioconda::biscuit=1.5.0.20240506
   - bioconda::samblaster=0.1.26
-  - bioconda::samtools=1.16.1
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/biscuit/biscuitblaster/main.nf b/modules/nf-core/biscuit/biscuitblaster/main.nf
index c4f7e1a52c5..f7876cb2fb5 100644
--- a/modules/nf-core/biscuit/biscuitblaster/main.nf
+++ b/modules/nf-core/biscuit/biscuitblaster/main.nf
@@ -4,12 +4,13 @@ process BISCUIT_BLASTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-d94f582b04a3edcede1215189c0d881506640fd9:6519548ea4f3d6a526c78ad0350c58f867f28574-0':
-        'biocontainers/mulled-v2-d94f582b04a3edcede1215189c0d881506640fd9:6519548ea4f3d6a526c78ad0350c58f867f28574-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/22/22f141a92e12f98040054b9a47a51fb4de9c544174bbfa6d251a110f5e26fddc/data':
+        'community.wave.seqera.io/library/biscuit_samblaster_samtools:a683d0887e7a91bf' }"
 
     input:
     tuple val(meta), path(reads)
-    path index
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(index)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -24,23 +25,24 @@ process BISCUIT_BLASTER {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def args3 = task.ext.args3 ?: ''
-    def biscuit_cpus = (int) Math.max(Math.floor(task.cpus*0.95),1)
-    def samtools_cpus = task.cpus-biscuit_cpus
+    def biscuit_cpus = [(task.cpus * 0.9) as int, 1].max()
+    def samtools_cpus = (task.cpus - biscuit_cpus < 1) ? biscuit_cpus : (task.cpus - biscuit_cpus)
     """
-    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/\\.bis.amb\$//'`
+    ln -sf \$(readlink $fasta) $index/$fasta
 
     biscuit align \\
         -@ $biscuit_cpus \\
         $args \\
-        \$INDEX \\
-        $reads | \\
-    samblaster \\
-        $args2 | \\
-    samtools sort \\
-        -@ $samtools_cpus \\
-        $args3 \\
-        --write-index \\
-        -o ${prefix}.bam##idx##${prefix}.bam.bai
+        $index/$fasta\\
+        $reads \\
+        | samblaster $args2 \\
+        | samtools sort \\
+            -@ $samtools_cpus \\
+            $args3 \\
+            --write-index \\
+            -o ${prefix}.bam -O BAM -
+
+    samtools index ${prefix}.bam
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/biscuit/biscuitblaster/meta.yml b/modules/nf-core/biscuit/biscuitblaster/meta.yml
index d64cc1c2694..f2bed154053 100644
--- a/modules/nf-core/biscuit/biscuitblaster/meta.yml
+++ b/modules/nf-core/biscuit/biscuitblaster/meta.yml
@@ -1,6 +1,5 @@
 name: biscuit_blaster
-description: A fast, compact one-liner to produce duplicate-marked, sorted, and indexed
-  BAM files using Biscuit
+description: A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit
 keywords:
   - biscuit
   - DNA methylation
@@ -48,12 +47,24 @@ input:
     - reads:
         type: file
         description: |
-          List of input fastq files of size 1 and 2 for single-end and paired-end data,
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
-  - - index:
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - index:
         type: directory
-        description: Biscuit genome index directory (generated with 'biscuit index')
-        pattern: "BiscuitIndex"
+        description: Directory containing biscuit genome index
 output:
   - bam:
       - meta:
@@ -84,3 +95,4 @@ authors:
   - "@njspix"
 maintainers:
   - "@njspix"
+  - "@sateeshperi"
diff --git a/modules/nf-core/biscuit/biscuitblaster/tests/main.nf.test b/modules/nf-core/biscuit/biscuitblaster/tests/main.nf.test
index ccea7f5b85e..9b7f7562ed8 100644
--- a/modules/nf-core/biscuit/biscuitblaster/tests/main.nf.test
+++ b/modules/nf-core/biscuit/biscuitblaster/tests/main.nf.test
@@ -14,21 +14,27 @@ nextflow_process {
             script "../../index/main.nf"
             process {
             """
-            input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+            input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+            ])
             """
             }
         }
     }
 
-    test("sarscov2 - single") {
+    test("sarscov2 single-end [fastq_gz]") {
         when {
             process {
                 """
                 input[0] = [ [ id:'test' ], // meta map
                                 [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz", checkIfExists: true) ]
-                            ]
-
-                input[1] = BISCUIT_INDEX.out.index
+                ]
+                input[1] = Channel.of([
+                                [ id:'test' ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -36,25 +42,30 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(file(process.out.bai[0][1]).name,
-                                  process.out.bam.collect { bam(it[1]).getHeaderMD5() },
-                                  process.out.bam.collect { bam(it[1]).getReadsMD5() },
-                                  process.out.versions).match() }
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+                    process.out.bai,
+					process.out.versions
+					).match()
+				}
             )
         }
 
     }
 
-    test("sarscov2 - paired-end") {
+    test("sarscov2 paired-end [fastq_gz]") {
         when {
             process {
                 """
                 input[0] = [ [ id:'test' ], // meta map
                                 [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz", checkIfExists: true),
                                   file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz", checkIfExists: true) ]
-                            ]
-
-                input[1] = BISCUIT_INDEX.out.index
+                ]
+                input[1] = Channel.of([
+                                [ id:'test' ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -62,15 +73,17 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.bai,
-                                  process.out.bam.collect { bam(it[1]).getHeaderMD5() },
-                                  process.out.bam.collect { bam(it[1]).getReadsMD5() },
-                                  process.out.versions).match() }
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+                    process.out.bai,
+					process.out.versions
+					).match()
+				}
             )
         }
     }
 
-    test("sarscov2 - paired-end -stub") {
+    test("sarscov2 paired-end [fastq_gz] - stub") {
         options "-stub"
         when {
             process {
@@ -78,9 +91,12 @@ nextflow_process {
                 input[0] = [ [ id:'test' ], // meta map
                                 [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz", checkIfExists: true),
                                   file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz", checkIfExists: true) ]
-                            ]
-
-                input[1] = BISCUIT_INDEX.out.index
+                ]
+                input[1] = Channel.of([
+                                [ id:'test' ], // meta map
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
                 """
             }
         }
diff --git a/modules/nf-core/biscuit/biscuitblaster/tests/main.nf.test.snap b/modules/nf-core/biscuit/biscuitblaster/tests/main.nf.test.snap
index e537de7d8ca..72f3eea613f 100644
--- a/modules/nf-core/biscuit/biscuitblaster/tests/main.nf.test.snap
+++ b/modules/nf-core/biscuit/biscuitblaster/tests/main.nf.test.snap
@@ -1,50 +1,47 @@
 {
-    "sarscov2 - single": {
+    "sarscov2 single-end [fastq_gz]": {
         "content": [
-            "test.bam.bai",
+            "499055250804bb3674c724bd9adf9d02",
             [
-                "a3b85097046b61879ab72293c38daea0"
-            ],
-            [
-                "499055250804bb3674c724bd9adf9d02"
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.bam.bai:md5,56efb7d64af887266e8490a4afd6171f"
+                ]
             ],
             [
-                "versions.yml:md5,3f08154389b908fdfee5d4a328781e96"
+                "versions.yml:md5,92fe349c3b2cd12866273c14f89d79b9"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-10T11:20:35.533081588"
+        "timestamp": "2024-11-14T06:39:47.556767238"
     },
-    "sarscov2 - paired-end": {
+    "sarscov2 paired-end [fastq_gz]": {
         "content": [
+            "6b5afc62da5533472e1479950bb5f09a",
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test.bam.bai:md5,bc235b43786886957bd5bb5b6623d4dd"
+                    "test.bam.bai:md5,128302694afc1cf9e04b45c41860785f"
                 ]
             ],
             [
-                "d66c238598e02630bba7595baa2a6e71"
-            ],
-            [
-                "6b5afc62da5533472e1479950bb5f09a"
-            ],
-            [
-                "versions.yml:md5,3f08154389b908fdfee5d4a328781e96"
+                "versions.yml:md5,92fe349c3b2cd12866273c14f89d79b9"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-10T10:57:59.954913657"
+        "timestamp": "2024-11-14T06:40:01.376002655"
     },
-    "sarscov2 - paired-end -stub": {
+    "sarscov2 paired-end [fastq_gz] - stub": {
         "content": [
             {
                 "0": [
@@ -64,7 +61,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,3f08154389b908fdfee5d4a328781e96"
+                    "versions.yml:md5,92fe349c3b2cd12866273c14f89d79b9"
                 ],
                 "bai": [
                     [
@@ -83,14 +80,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3f08154389b908fdfee5d4a328781e96"
+                    "versions.yml:md5,92fe349c3b2cd12866273c14f89d79b9"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-10T10:58:19.26950429"
+        "timestamp": "2024-11-14T06:40:14.345664344"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/biscuit/biscuitblaster/tests/tags.yml b/modules/nf-core/biscuit/biscuitblaster/tests/tags.yml
deleted file mode 100644
index 13adde05efb..00000000000
--- a/modules/nf-core/biscuit/biscuitblaster/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-biscuit/biscuitblaster:
-  - "modules/nf-core/biscuit/biscuitblaster/**"
diff --git a/modules/nf-core/biscuit/bsconv/environment.yml b/modules/nf-core/biscuit/bsconv/environment.yml
index 56b7e967693..123215dc20f 100644
--- a/modules/nf-core/biscuit/bsconv/environment.yml
+++ b/modules/nf-core/biscuit/bsconv/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::biscuit=1.1.0.20220707
+  - bioconda::biscuit=1.5.0.20240506
diff --git a/modules/nf-core/biscuit/bsconv/main.nf b/modules/nf-core/biscuit/bsconv/main.nf
index 881fa0be813..5fb47439d1c 100644
--- a/modules/nf-core/biscuit/bsconv/main.nf
+++ b/modules/nf-core/biscuit/bsconv/main.nf
@@ -2,18 +2,19 @@ process BISCUIT_BSCONV {
     tag "$meta.id"
     label 'process_long'
 
-
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/biscuit:1.1.0.20220707--he272189_1':
-        'biocontainers/biscuit:1.1.0.20220707--he272189_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/33/33a9ca30b4154f11253c8d91a75382065dcb8282ba99b74dbee59ed8faceabd7/data':
+        'community.wave.seqera.io/library/biscuit:1.5.0.20240506--ca92d9d0a37b5fa8' }"
 
     input:
-    tuple val(meta), path(bam), path(bai)
-    path(index)
+    tuple val(meta), path(bam)
+    tuple val(meta2), path(bai)
+    tuple val(meta3), path(fasta)
+    tuple val(meta4), path(index)
 
     output:
-    tuple val(meta), path("*.bam"), emit: bsconv_bam
+    tuple val(meta), path("*.bam"), emit: bam
     path "versions.yml"           , emit: versions
 
     when:
@@ -24,11 +25,11 @@ process BISCUIT_BSCONV {
     def prefix = task.ext.prefix ?: "${meta.id}"
     if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
-    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/\\.bis.amb\$//'`
+    ln -sf \$(readlink $fasta) $index/$fasta
 
     biscuit bsconv \\
         $args \\
-        \$INDEX \\
+        $index/$fasta \\
         $bam \\
         ${prefix}.bam
 
@@ -41,8 +42,6 @@ process BISCUIT_BSCONV {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if ("$bam" == "${prefix}.bam") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
-
     """
     touch ${prefix}.bam
 
diff --git a/modules/nf-core/biscuit/bsconv/meta.yml b/modules/nf-core/biscuit/bsconv/meta.yml
index 75d9b2b7939..e162e175af0 100644
--- a/modules/nf-core/biscuit/bsconv/meta.yml
+++ b/modules/nf-core/biscuit/bsconv/meta.yml
@@ -27,15 +27,32 @@ input:
     - bam:
         type: file
         description: BAM file contained mapped reads
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
     - bai:
         type: file
         description: BAM file index
-  - - index:
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - index:
         type: directory
-        description: Biscuit genome index directory (generated with 'biscuit index')
-        pattern: "BiscuitIndex"
+        description: Directory containing biscuit genome index
 output:
-  - bsconv_bam:
+  - bam:
       - meta:
           type: map
           description: |
@@ -54,3 +71,4 @@ authors:
   - "@njspix"
 maintainers:
   - "@njspix"
+  - "@sateeshperi"
diff --git a/modules/nf-core/biscuit/bsconv/tests/main.nf.test b/modules/nf-core/biscuit/bsconv/tests/main.nf.test
index 1cbf306a88b..331c3df01f8 100644
--- a/modules/nf-core/biscuit/bsconv/tests/main.nf.test
+++ b/modules/nf-core/biscuit/bsconv/tests/main.nf.test
@@ -9,29 +9,36 @@ nextflow_process {
     tag "biscuit/bsconv"
     tag "biscuit/index"
 
-
     setup {
         run("BISCUIT_INDEX") {
             script "../../index/main.nf"
             process {
             """
-            input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+            input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+            ])
             """
             }
         }
     }
 
-    test("sarscov2-pe - bam") {
+    test("sarscov2 paired-end [bam]") {
 
         when {
             process {
                 """
                 input[0] = [ [id:'test', single_end:false ], // meta map
-                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = [ [id:'test', single_end:false ], // meta map
                             file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
-                            ]
-
-                input[1] = BISCUIT_INDEX.out.index
+                ]
+                input[2] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[3] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -39,14 +46,17 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.bsconv_bam).match("bsconv_bam") },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
             )
         }
 
     }
 
-    test("sarscov2-pe - bam - stub") {
+    test("sarscov2 paired-end [bam] - stub") {
 
         options "-stub"
 
@@ -54,11 +64,16 @@ nextflow_process {
             process {
                 """
                 input[0] = [ [id:'test', single_end:false ], // meta map
-                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = [ [id:'test', single_end:false ], // meta map
                             file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
-                            ]
-
-                input[1] = BISCUIT_INDEX.out.index
+                ]
+                input[2] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[3] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -66,7 +81,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+					bam(process.out.bam[0][1]).getReadsMD5(),
+					process.out.versions
+					).match()
+				}
             )
         }
 
diff --git a/modules/nf-core/biscuit/bsconv/tests/main.nf.test.snap b/modules/nf-core/biscuit/bsconv/tests/main.nf.test.snap
index 96dc77c097b..7796ebbb5ad 100644
--- a/modules/nf-core/biscuit/bsconv/tests/main.nf.test.snap
+++ b/modules/nf-core/biscuit/bsconv/tests/main.nf.test.snap
@@ -1,67 +1,28 @@
 {
-    "versions": {
+    "sarscov2 paired-end [bam]": {
         "content": [
+            "1608a01cabbbaba635e2905b7049f487",
             [
-                "versions.yml:md5,45455cc9522a3235fa482ad065a242b3"
+                "versions.yml:md5,f8bba061ed5d28794abb4ffc2898aa02"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-07T15:28:04.601734997"
+        "timestamp": "2024-11-14T08:18:08.129627771"
     },
-    "sarscov2-pe - bam - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,45455cc9522a3235fa482ad065a242b3"
-                ],
-                "bsconv_bam": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,45455cc9522a3235fa482ad065a242b3"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-05-07T15:28:14.729945289"
-    },
-    "bsconv_bam": {
+    "sarscov2 paired-end [bam] - stub": {
         "content": [
+            "d41d8cd98f00b204e9800998ecf8427e",
             [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test.bam:md5,0d425851bd18963ebf1b6d727a7d02c7"
-                ]
+                "versions.yml:md5,f8bba061ed5d28794abb4ffc2898aa02"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-07T15:28:04.580771449"
+        "timestamp": "2024-11-14T08:18:18.658974235"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/biscuit/bsconv/tests/tags.yml b/modules/nf-core/biscuit/bsconv/tests/tags.yml
deleted file mode 100644
index 5b890ac3597..00000000000
--- a/modules/nf-core/biscuit/bsconv/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-biscuit/bsconv:
-  - "modules/nf-core/biscuit/bsconv/**"
diff --git a/modules/nf-core/biscuit/epiread/environment.yml b/modules/nf-core/biscuit/epiread/environment.yml
index b4bab59944c..222c156ed9a 100644
--- a/modules/nf-core/biscuit/epiread/environment.yml
+++ b/modules/nf-core/biscuit/epiread/environment.yml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::biscuit=1.1.0.20220707
-  - bioconda::samtools=1.16.1
+  - bioconda::biscuit=1.5.0.20240506
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/biscuit/epiread/main.nf b/modules/nf-core/biscuit/epiread/main.nf
index 8eeb675c09c..110177c000c 100644
--- a/modules/nf-core/biscuit/epiread/main.nf
+++ b/modules/nf-core/biscuit/epiread/main.nf
@@ -4,15 +4,18 @@ process BISCUIT_EPIREAD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-d94f582b04a3edcede1215189c0d881506640fd9:6519548ea4f3d6a526c78ad0350c58f867f28574-0':
-        'biocontainers/mulled-v2-d94f582b04a3edcede1215189c0d881506640fd9:6519548ea4f3d6a526c78ad0350c58f867f28574-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5b/5b542bbe1f99afd494ef07423ea8b52f2b8a081b85f92db2726c283c78da3cf0/data':
+        'community.wave.seqera.io/library/biscuit_samtools:84373c8a97fa63b8' }"
 
     input:
-    tuple val(meta), path(bam), path(bai), path(snp_bed)
-    path(index)
+    tuple val(meta), path(bam)
+    tuple val(meta2), path(bai)
+    tuple val(meta3), path(snp_bed)
+    tuple val(meta4), path(fasta)
+    tuple val(meta5), path(index)
 
     output:
-    tuple val(meta), path("*.bed.gz"), emit: epiread_bed
+    tuple val(meta), path("*.bed.gz"), emit: bed
     path "versions.yml"              , emit: versions
 
     when:
@@ -22,8 +25,8 @@ process BISCUIT_EPIREAD {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def biscuit_cpus = (int) Math.max(Math.floor(task.cpus*0.9),1)
-    def samtools_cpus = task.cpus-biscuit_cpus
+    def biscuit_cpus = [(task.cpus * 0.9) as int, 1].max()
+    def samtools_cpus = (task.cpus - biscuit_cpus < 1) ? biscuit_cpus : (task.cpus - biscuit_cpus)
     // As of 2/25/22, epiread does not support reading a gzipped SNP BED file.
     // This is a bit hacky but allows the user to supply a gzipped OR uncompressed bed file
     def unzip_snp_bed = snp_bed && (snp_bed.toString() =~ /\.gz$/) ? "bgzip -d ${snp_bed}" : ""
@@ -32,7 +35,7 @@ process BISCUIT_EPIREAD {
     def options_snp_bed = snp_bed ? "-B ${unzipped_snp_bed}" : ""
     if ("$options_snp_bed" == "${prefix}.bed.gz") error "Input and output names for biscuit epiread are the same, set prefix in module configuration to disambiguate!"
     """
-    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/\\.bis.amb\$//'`
+    ln -sf \$(readlink $fasta) $index/$fasta
 
     $unzip_snp_bed
 
@@ -40,11 +43,10 @@ process BISCUIT_EPIREAD {
         -@ $biscuit_cpus \\
         $args \\
         $options_snp_bed \\
-        \$INDEX \\
-        $bam | \\
-    LC_ALL=C sort -k1,1 -k2,2n | \\
-    bgzip \\
-        -@ $samtools_cpus \\
+        $index/$fasta \\
+        $bam \\
+        | LC_ALL=C sort -k1,1 -k2,2n \\
+        | bgzip -@ $samtools_cpus \\
         $args2 \\
         -c > ${prefix}.bed.gz
 
@@ -57,9 +59,6 @@ process BISCUIT_EPIREAD {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def unzipped_snp_bed = snp_bed ? snp_bed.toString() - ~/\.gz$/: ""
-    def options_snp_bed = snp_bed ? "-B ${unzipped_snp_bed}" : ""
-    if ("$options_snp_bed" == "${prefix}.bed.gz") error "Input and output names for biscuit epiread are the same, set prefix in module configuration to disambiguate!"
     """
     echo | gzip > ${prefix}.bed.gz
 
diff --git a/modules/nf-core/biscuit/epiread/meta.yml b/modules/nf-core/biscuit/epiread/meta.yml
index 8974f1d952a..b695be1cd8f 100644
--- a/modules/nf-core/biscuit/epiread/meta.yml
+++ b/modules/nf-core/biscuit/epiread/meta.yml
@@ -27,19 +27,41 @@ input:
           e.g. [ id:'test', single_end:false ]
     - bam:
         type: file
-        description: Biscuit BAM file
+        description: BAM file contained mapped reads
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
     - bai:
         type: file
-        description: BAM index
+        description: BAM file index
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
     - snp_bed:
         type: file
         description: BED file containing SNP information (optional)
-  - - index:
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+  - - meta5:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - index:
         type: directory
-        description: Biscuit genome index directory (generated with 'biscuit index')
-        pattern: "BiscuitIndex"
+        description: Directory containing biscuit genome index
 output:
-  - epiread_bed:
+  - bed:
       - meta:
           type: map
           description: |
@@ -58,3 +80,4 @@ authors:
   - "@njspix"
 maintainers:
   - "@njspix"
+  - "@sateeshperi"
diff --git a/modules/nf-core/biscuit/epiread/tests/main.nf.test b/modules/nf-core/biscuit/epiread/tests/main.nf.test
index 5a151008afa..ceb1bff5b6f 100644
--- a/modules/nf-core/biscuit/epiread/tests/main.nf.test
+++ b/modules/nf-core/biscuit/epiread/tests/main.nf.test
@@ -15,24 +15,36 @@ nextflow_process {
             script "../../index/main.nf"
             process {
                 """
-                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
                 """
             }
         }
     }
 
-    test("sarscov2 - test_paired_end_methylated_sorted_bam") {
+    test("sarscov2 paired-end [bam]") {
 
         when {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true),
-                    [] //SNP BED file
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true)
                 ]
-                input[1] = BISCUIT_INDEX.out.index
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'test' ], [] //SNP BED file
+                ]
+                input[3] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[4] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -46,18 +58,28 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - test_paired_end_methylated_sorted_bam - snp") {
+    test("sarscov2 paired-end [bam] [snp]") {
 
         when {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true),
-                    file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed')
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'test' ],
+                    file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed', checkIfExists: true)
                 ]
-                input[1] = BISCUIT_INDEX.out.index
+                input[3] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[4] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -71,18 +93,28 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - test_paired_end_methylated_sorted_bam - snp - gz") {
+    test("sarscov2 paired-end [bam] [snp_gz]") {
 
         when {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true),
-                    file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed.gz')
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true)
                 ]
-                input[1] = BISCUIT_INDEX.out.index
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'test' ],
+                    file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed.gz', checkIfExists: true)
+                ]
+                input[3] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[4] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -96,19 +128,29 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - test_paired_end_methylated_sorted_bam - snp - gz - stub") {
+    test("sarscov2 paired-end [bam] [snp_gz] - stub") {
         options '-stub'
 
         when {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true),
-                    file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed.gz')
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'test' ],
+                    file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test-snp.bed.gz', checkIfExists: true)
                 ]
-                input[1] = BISCUIT_INDEX.out.index
+                input[3] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[4] = BISCUIT_INDEX.out.index
                 """
             }
         }
diff --git a/modules/nf-core/biscuit/epiread/tests/main.nf.test.snap b/modules/nf-core/biscuit/epiread/tests/main.nf.test.snap
index 1a64679d465..19a1e069912 100644
--- a/modules/nf-core/biscuit/epiread/tests/main.nf.test.snap
+++ b/modules/nf-core/biscuit/epiread/tests/main.nf.test.snap
@@ -1,142 +1,134 @@
 {
-    "sarscov2 - test_paired_end_methylated_sorted_bam - snp - gz": {
+    "sarscov2 paired-end [bam] [snp_gz]": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test.bed.gz:md5,f2c701470965f9a93c45524e9e460509"
+                        "test.bed.gz:md5,709eeae76ae45a08983e8b45e183dad8"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,aba0dae715c3208d621eff05bfff02d3"
+                    "versions.yml:md5,e8b0e104428b24831e25ae3d6844aaae"
                 ],
-                "epiread_bed": [
+                "bed": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test.bed.gz:md5,f2c701470965f9a93c45524e9e460509"
+                        "test.bed.gz:md5,709eeae76ae45a08983e8b45e183dad8"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aba0dae715c3208d621eff05bfff02d3"
+                    "versions.yml:md5,e8b0e104428b24831e25ae3d6844aaae"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-29T11:55:24.162952"
+        "timestamp": "2024-11-14T08:58:54.313858378"
     },
-    "sarscov2 - test_paired_end_methylated_sorted_bam - snp": {
+    "sarscov2 paired-end [bam]": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test.bed.gz:md5,f2c701470965f9a93c45524e9e460509"
+                        "test.bed.gz:md5,f75d8fe928fe2dc1a3ce6178d8963602"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,aba0dae715c3208d621eff05bfff02d3"
+                    "versions.yml:md5,e8b0e104428b24831e25ae3d6844aaae"
                 ],
-                "epiread_bed": [
+                "bed": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test.bed.gz:md5,f2c701470965f9a93c45524e9e460509"
+                        "test.bed.gz:md5,f75d8fe928fe2dc1a3ce6178d8963602"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aba0dae715c3208d621eff05bfff02d3"
+                    "versions.yml:md5,e8b0e104428b24831e25ae3d6844aaae"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-29T11:55:17.32731"
+        "timestamp": "2024-11-14T08:58:32.745357698"
     },
-    "sarscov2 - test_paired_end_methylated_sorted_bam": {
+    "sarscov2 paired-end [bam] [snp]": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test.bed.gz:md5,3f60061464bd1c282bce0dc6478f8738"
+                        "test.bed.gz:md5,709eeae76ae45a08983e8b45e183dad8"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,aba0dae715c3208d621eff05bfff02d3"
+                    "versions.yml:md5,e8b0e104428b24831e25ae3d6844aaae"
                 ],
-                "epiread_bed": [
+                "bed": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test.bed.gz:md5,3f60061464bd1c282bce0dc6478f8738"
+                        "test.bed.gz:md5,709eeae76ae45a08983e8b45e183dad8"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aba0dae715c3208d621eff05bfff02d3"
+                    "versions.yml:md5,e8b0e104428b24831e25ae3d6844aaae"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-29T11:55:09.919651"
+        "timestamp": "2024-11-14T08:58:43.662473332"
     },
-    "sarscov2 - test_paired_end_methylated_sorted_bam - snp - gz - stub": {
+    "sarscov2 paired-end [bam] [snp_gz] - stub": {
         "content": [
             {
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,aba0dae715c3208d621eff05bfff02d3"
+                    "versions.yml:md5,e8b0e104428b24831e25ae3d6844aaae"
                 ],
-                "epiread_bed": [
+                "bed": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,aba0dae715c3208d621eff05bfff02d3"
+                    "versions.yml:md5,e8b0e104428b24831e25ae3d6844aaae"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-29T11:55:29.932067"
+        "timestamp": "2024-11-14T08:59:04.687765786"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/biscuit/index/environment.yml b/modules/nf-core/biscuit/index/environment.yml
index 56b7e967693..123215dc20f 100644
--- a/modules/nf-core/biscuit/index/environment.yml
+++ b/modules/nf-core/biscuit/index/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::biscuit=1.1.0.20220707
+  - bioconda::biscuit=1.5.0.20240506
diff --git a/modules/nf-core/biscuit/index/main.nf b/modules/nf-core/biscuit/index/main.nf
index 43566fc4b50..fb5ab0d40c5 100644
--- a/modules/nf-core/biscuit/index/main.nf
+++ b/modules/nf-core/biscuit/index/main.nf
@@ -4,15 +4,15 @@ process BISCUIT_INDEX {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/biscuit:1.1.0.20220707--he272189_1':
-        'biocontainers/biscuit:1.1.0.20220707--he272189_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/33/33a9ca30b4154f11253c8d91a75382065dcb8282ba99b74dbee59ed8faceabd7/data':
+        'community.wave.seqera.io/library/biscuit:1.5.0.20240506--ca92d9d0a37b5fa8' }"
 
     input:
-    path fasta, stageAs: "BiscuitIndex/*"
+    tuple val(meta), path(fasta, name:"BiscuitIndex/")
 
     output:
-    path "BiscuitIndex/*.fa*", emit: index, includeInputs: true
-    path "versions.yml"      , emit: versions
+    tuple val(meta), path("BiscuitIndex"), emit: index
+    path "versions.yml"                  , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -34,7 +34,6 @@ process BISCUIT_INDEX {
     stub:
     def args = task.ext.args ?: ''
     """
-
     touch ${fasta}.bis.amb
     touch ${fasta}.bis.ann
     touch ${fasta}.bis.pac
diff --git a/modules/nf-core/biscuit/index/meta.yml b/modules/nf-core/biscuit/index/meta.yml
index 39a0bcf8d94..cdf51a8b4d6 100644
--- a/modules/nf-core/biscuit/index/meta.yml
+++ b/modules/nf-core/biscuit/index/meta.yml
@@ -19,15 +19,24 @@ tools:
       licence: ["MIT"]
       identifier: biotools:biscuit
 input:
-  - - fasta:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
         type: file
         description: Input genome fasta file
 output:
   - index:
-      - BiscuitIndex/*.fa*:
+      - meta:
           type: directory
-          description: Biscuit genome index directory
-          pattern: "BiscuitIndex"
+          description: Directory containing biscuit genome index
+          pattern: "index"
+      - BiscuitIndex:
+          type: directory
+          description: Directory containing biscuit genome index
+          pattern: "index"
   - versions:
       - versions.yml:
           type: file
@@ -37,3 +46,4 @@ authors:
   - "@njspix"
 maintainers:
   - "@njspix"
+  - "@sateeshperi"
diff --git a/modules/nf-core/biscuit/index/tests/main.nf.test b/modules/nf-core/biscuit/index/tests/main.nf.test
index 0402a262200..3c99b27bb08 100644
--- a/modules/nf-core/biscuit/index/tests/main.nf.test
+++ b/modules/nf-core/biscuit/index/tests/main.nf.test
@@ -1,4 +1,3 @@
-
 nextflow_process {
 
     name "Test Process BISCUIT_INDEX"
@@ -10,13 +9,15 @@ nextflow_process {
     tag "biscuit"
     tag "biscuit/index"
 
-    test("test-biscuit-index") {
+    test("sarscov2 genome [fasta]") {
 
         when {
             process {
                 """
-                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
                 """
             }
         }
@@ -29,14 +30,16 @@ nextflow_process {
         }
     }
 
-    test("test-biscuit-index-stub") {
+    test("sarscov2 genome [fasta] - stub") {
         options '-stub'
 
         when {
             process {
                 """
-                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
-
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
                 """
             }
         }
diff --git a/modules/nf-core/biscuit/index/tests/main.nf.test.snap b/modules/nf-core/biscuit/index/tests/main.nf.test.snap
index 698fc7e4bd8..715875012bd 100644
--- a/modules/nf-core/biscuit/index/tests/main.nf.test.snap
+++ b/modules/nf-core/biscuit/index/tests/main.nf.test.snap
@@ -1,84 +1,104 @@
 {
-    "test-biscuit-index": {
+    "sarscov2 genome [fasta] - stub": {
         "content": [
             {
                 "0": [
                     [
-                        "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
-                        "genome.fasta.bis.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e",
-                        "genome.fasta.bis.ann:md5,c32e11f6c859f166c7525a9c1d583567",
-                        "genome.fasta.bis.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66",
-                        "genome.fasta.dau.bwt:md5,a11bc31775f7b7a4f9cd3bc4f981661a",
-                        "genome.fasta.dau.sa:md5,9c9e07fa1c75ef32d764274579c89b08",
-                        "genome.fasta.par.bwt:md5,62eb83cd557a47b59589713d98024fc2",
-                        "genome.fasta.par.sa:md5,55bcd97d7059bf73dc0d221e36e8e901"
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
+                            "genome.fasta.bis.amb:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.bis.ann:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.bis.pac:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.dau.bwt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.dau.sa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.par.bwt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.par.sa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,067af0790b982d7524b24ba17e1dece7"
+                    "versions.yml:md5,c451c038f5d41cd7237c5b0f07926ad6"
                 ],
                 "index": [
                     [
-                        "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
-                        "genome.fasta.bis.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e",
-                        "genome.fasta.bis.ann:md5,c32e11f6c859f166c7525a9c1d583567",
-                        "genome.fasta.bis.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66",
-                        "genome.fasta.dau.bwt:md5,a11bc31775f7b7a4f9cd3bc4f981661a",
-                        "genome.fasta.dau.sa:md5,9c9e07fa1c75ef32d764274579c89b08",
-                        "genome.fasta.par.bwt:md5,62eb83cd557a47b59589713d98024fc2",
-                        "genome.fasta.par.sa:md5,55bcd97d7059bf73dc0d221e36e8e901"
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
+                            "genome.fasta.bis.amb:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.bis.ann:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.bis.pac:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.dau.bwt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.dau.sa:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.par.bwt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "genome.fasta.par.sa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,067af0790b982d7524b24ba17e1dece7"
+                    "versions.yml:md5,c451c038f5d41cd7237c5b0f07926ad6"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-28T10:33:50.146795"
+        "timestamp": "2024-11-13T06:48:54.473235719"
     },
-    "test-biscuit-index-stub": {
+    "sarscov2 genome [fasta]": {
         "content": [
             {
                 "0": [
                     [
-                        "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
-                        "genome.fasta.bis.amb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.bis.ann:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.bis.pac:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.dau.bwt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.dau.sa:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.par.bwt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.par.sa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
+                            "genome.fasta.bis.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e",
+                            "genome.fasta.bis.ann:md5,c32e11f6c859f166c7525a9c1d583567",
+                            "genome.fasta.bis.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66",
+                            "genome.fasta.dau.bwt:md5,a11bc31775f7b7a4f9cd3bc4f981661a",
+                            "genome.fasta.dau.sa:md5,9c9e07fa1c75ef32d764274579c89b08",
+                            "genome.fasta.par.bwt:md5,62eb83cd557a47b59589713d98024fc2",
+                            "genome.fasta.par.sa:md5,55bcd97d7059bf73dc0d221e36e8e901"
+                        ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,067af0790b982d7524b24ba17e1dece7"
+                    "versions.yml:md5,c451c038f5d41cd7237c5b0f07926ad6"
                 ],
                 "index": [
                     [
-                        "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
-                        "genome.fasta.bis.amb:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.bis.ann:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.bis.pac:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.dau.bwt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.dau.sa:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.par.bwt:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "genome.fasta.par.sa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6",
+                            "genome.fasta.bis.amb:md5,3a68b8b2287e07dd3f5f95f4344ba76e",
+                            "genome.fasta.bis.ann:md5,c32e11f6c859f166c7525a9c1d583567",
+                            "genome.fasta.bis.pac:md5,983e3d2cd6f36e2546e6d25a0da78d66",
+                            "genome.fasta.dau.bwt:md5,a11bc31775f7b7a4f9cd3bc4f981661a",
+                            "genome.fasta.dau.sa:md5,9c9e07fa1c75ef32d764274579c89b08",
+                            "genome.fasta.par.bwt:md5,62eb83cd557a47b59589713d98024fc2",
+                            "genome.fasta.par.sa:md5,55bcd97d7059bf73dc0d221e36e8e901"
+                        ]
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,067af0790b982d7524b24ba17e1dece7"
+                    "versions.yml:md5,c451c038f5d41cd7237c5b0f07926ad6"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-29T10:49:18.069711"
+        "timestamp": "2024-11-13T06:48:44.596263127"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/biscuit/mergecg/environment.yml b/modules/nf-core/biscuit/mergecg/environment.yml
index b4bab59944c..222c156ed9a 100644
--- a/modules/nf-core/biscuit/mergecg/environment.yml
+++ b/modules/nf-core/biscuit/mergecg/environment.yml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::biscuit=1.1.0.20220707
-  - bioconda::samtools=1.16.1
+  - bioconda::biscuit=1.5.0.20240506
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/biscuit/mergecg/main.nf b/modules/nf-core/biscuit/mergecg/main.nf
index 93094b2a6cd..14efa0b7d81 100644
--- a/modules/nf-core/biscuit/mergecg/main.nf
+++ b/modules/nf-core/biscuit/mergecg/main.nf
@@ -4,16 +4,17 @@ process BISCUIT_MERGECG {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-d94f582b04a3edcede1215189c0d881506640fd9:6519548ea4f3d6a526c78ad0350c58f867f28574-0':
-        'biocontainers/mulled-v2-d94f582b04a3edcede1215189c0d881506640fd9:6519548ea4f3d6a526c78ad0350c58f867f28574-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5b/5b542bbe1f99afd494ef07423ea8b52f2b8a081b85f92db2726c283c78da3cf0/data':
+        'community.wave.seqera.io/library/biscuit_samtools:84373c8a97fa63b8' }"
 
 
     input:
     tuple val(meta), path(bed)
-    path index
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(index)
 
     output:
-    tuple val(meta), path("*.bed.gz"), emit: mergecg_bed
+    tuple val(meta), path("*.bed.gz"), emit: bed
     path "versions.yml"              , emit: versions
 
     when:
@@ -24,16 +25,14 @@ process BISCUIT_MERGECG {
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/\\.bis.amb\$//'`
+    ln -sf \$(readlink $fasta) $index/$fasta
 
     biscuit mergecg \\
         $args \\
-        \$INDEX \\
-        $bed | \\
-    LC_ALL=C sort -k1,1 -k2,2n | \\
-    bgzip \\
-        $args2 \\
-        -c > ${prefix}.bed.gz
+        $index/$fasta\\
+        $bed \\
+        | LC_ALL=C sort -k1,1 -k2,2n \\
+        | bgzip $args2 -c > ${prefix}.bed.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/biscuit/mergecg/meta.yml b/modules/nf-core/biscuit/mergecg/meta.yml
index 2084f43b9d6..29b0889a4a1 100644
--- a/modules/nf-core/biscuit/mergecg/meta.yml
+++ b/modules/nf-core/biscuit/mergecg/meta.yml
@@ -27,12 +27,24 @@ input:
         type: file
         description: |
           Biscuit BED file (output of biscuit vcf2bed)
-  - - index:
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - index:
         type: directory
-        description: Biscuit genome index directory (generated with 'biscuit index')
-        pattern: "BiscuitIndex"
+        description: Directory containing biscuit genome index
 output:
-  - mergecg_bed:
+  - bed:
       - meta:
           type: map
           description: |
@@ -51,3 +63,4 @@ authors:
   - "@njspix"
 maintainers:
   - "@njspix"
+  - "@sateeshperi"
diff --git a/modules/nf-core/biscuit/mergecg/tests/main.nf.test b/modules/nf-core/biscuit/mergecg/tests/main.nf.test
index 0b593f76842..cfa29b719d9 100644
--- a/modules/nf-core/biscuit/mergecg/tests/main.nf.test
+++ b/modules/nf-core/biscuit/mergecg/tests/main.nf.test
@@ -9,27 +9,34 @@ nextflow_process {
     tag "biscuit/index"
     tag "biscuit/mergecg"
 
-    test("sars_cov_bed") {
-
-        setup {
+    setup {
             run("BISCUIT_INDEX") {
                 script "../../index/main.nf"
                 process {
                     """
-                    input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+                    input[0] = Channel.of([
+                        [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                    ])
                     """
                 }
             }
         }
+
+    test("sarscov2 cov [bed]") {
+
         when {
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
                             [ id:'test', single_end:false ], // meta map
                             file(params.modules_testdata_base_path + "delete_me/biscuit/test-cg.bed.gz", checkIfExists: true)
-                        ]
-
-                input[1] = BISCUIT_INDEX.out.index
+                ])
+                input[1] = Channel.of([
+                        [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -43,27 +50,21 @@ nextflow_process {
 
     }
 
-    test("sars_cov_bed -stub") {
+    test("sarscov2 cov [bed] - stub") {
         options "-stub"
-        setup {
-            run("BISCUIT_INDEX") {
-                script "../../index/main.nf"
-                process {
-                    """
-                    input[0] = file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
-                    """
-                }
-            }
-        }
+
         when {
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
                             [ id:'test', single_end:false ], // meta map
                             file(params.modules_testdata_base_path + "delete_me/biscuit/test-cg.bed.gz", checkIfExists: true)
-                        ]
-
-                input[1] = BISCUIT_INDEX.out.index
+                ])
+                input[1] = Channel.of([
+                        [ id:'test' ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
                 """
             }
         }
diff --git a/modules/nf-core/biscuit/mergecg/tests/main.nf.test.snap b/modules/nf-core/biscuit/mergecg/tests/main.nf.test.snap
index 148a1f947bd..f003dee7b8d 100644
--- a/modules/nf-core/biscuit/mergecg/tests/main.nf.test.snap
+++ b/modules/nf-core/biscuit/mergecg/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "sars_cov_bed": {
+    "sarscov2 cov [bed] - stub": {
         "content": [
             {
                 "0": [
@@ -8,33 +8,33 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.bed.gz:md5,8136632b0c17c61857a302a57ae302ef"
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,caa3e8096399d35c725d7e2d430605c9"
+                    "versions.yml:md5,4b2f3877d68071eafa0b0ec3e37c58a3"
                 ],
-                "mergecg_bed": [
+                "bed": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.bed.gz:md5,8136632b0c17c61857a302a57ae302ef"
+                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,caa3e8096399d35c725d7e2d430605c9"
+                    "versions.yml:md5,4b2f3877d68071eafa0b0ec3e37c58a3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-11T17:31:48.698330905"
+        "timestamp": "2024-11-14T09:09:45.257367761"
     },
-    "sars_cov_bed -stub": {
+    "sarscov2 cov [bed]": {
         "content": [
             {
                 "0": [
@@ -43,30 +43,30 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test.bed.gz:md5,8136632b0c17c61857a302a57ae302ef"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,caa3e8096399d35c725d7e2d430605c9"
+                    "versions.yml:md5,4b2f3877d68071eafa0b0ec3e37c58a3"
                 ],
-                "mergecg_bed": [
+                "bed": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test.bed.gz:md5,8136632b0c17c61857a302a57ae302ef"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,caa3e8096399d35c725d7e2d430605c9"
+                    "versions.yml:md5,4b2f3877d68071eafa0b0ec3e37c58a3"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-06-12T09:59:25.605969084"
+        "timestamp": "2024-11-14T09:09:30.544664794"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/biscuit/mergecg/tests/tags.yml b/modules/nf-core/biscuit/mergecg/tests/tags.yml
deleted file mode 100644
index d7140b07550..00000000000
--- a/modules/nf-core/biscuit/mergecg/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-biscuit/mergecg:
-  - "modules/nf-core/biscuit/mergecg/**"
diff --git a/modules/nf-core/biscuit/pileup/environment.yml b/modules/nf-core/biscuit/pileup/environment.yml
index b4bab59944c..222c156ed9a 100644
--- a/modules/nf-core/biscuit/pileup/environment.yml
+++ b/modules/nf-core/biscuit/pileup/environment.yml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::biscuit=1.1.0.20220707
-  - bioconda::samtools=1.16.1
+  - bioconda::biscuit=1.5.0.20240506
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/biscuit/pileup/main.nf b/modules/nf-core/biscuit/pileup/main.nf
index dbbd6ffa2d5..db51aae2c09 100644
--- a/modules/nf-core/biscuit/pileup/main.nf
+++ b/modules/nf-core/biscuit/pileup/main.nf
@@ -4,12 +4,13 @@ process BISCUIT_PILEUP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-d94f582b04a3edcede1215189c0d881506640fd9:6519548ea4f3d6a526c78ad0350c58f867f28574-0':
-        'biocontainers/mulled-v2-d94f582b04a3edcede1215189c0d881506640fd9:6519548ea4f3d6a526c78ad0350c58f867f28574-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5b/5b542bbe1f99afd494ef07423ea8b52f2b8a081b85f92db2726c283c78da3cf0/data':
+        'community.wave.seqera.io/library/biscuit_samtools:84373c8a97fa63b8' }"
 
     input:
     tuple val(meta), path(normal_bams), path(normal_bais), path(tumor_bam), path(tumor_bai)
-    path index
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(index)
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
@@ -22,18 +23,18 @@ process BISCUIT_PILEUP {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def biscuit_cpus = (int) Math.max(Math.floor(task.cpus*0.9),1)
-    def bgzip_cpus = task.cpus-biscuit_cpus
+    def biscuit_cpus = [(task.cpus * 0.9) as int, 1].max()
+    def bgzip_cpus = (task.cpus - biscuit_cpus < 1) ? biscuit_cpus : (task.cpus - biscuit_cpus)
     if ( tumor_bam != [] && normal_bams.toList().size() > 1 ) error "[BISCUIT_PILEUP] error: Tumor BAM provided with more than one normal BAM"
     if ( tumor_bam.toList().size() > 1 ) error "[BISCUIT_PILEUP] error: more than one tumor BAM provided"
     input = ( tumor_bam==[] ) ? "${normal_bams}" : "-S -T ${tumor_bam} -I ${normal_bams}"
     """
-    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/\\.bis.amb\$//'`
+    ln -sf \$(readlink $fasta) $index/$fasta
 
     biscuit pileup \\
         -@ $biscuit_cpus \\
         $args \\
-        \$INDEX \\
+        $index/$fasta \\
         $input \\
         | bgzip -@ $bgzip_cpus $args2 > ${prefix}.vcf.gz
 
diff --git a/modules/nf-core/biscuit/pileup/meta.yml b/modules/nf-core/biscuit/pileup/meta.yml
index 9f532797e43..0ab31cc549b 100644
--- a/modules/nf-core/biscuit/pileup/meta.yml
+++ b/modules/nf-core/biscuit/pileup/meta.yml
@@ -47,10 +47,22 @@ input:
         type: file
         description: Optional. BAM index file corresponding to provided tumor_bam
         pattern: "*.{bai}"
-  - - index:
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: Input genome fasta file
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - index:
         type: directory
-        description: Biscuit genome index directory (generated with 'biscuit index')
-        pattern: "BiscuitIndex"
+        description: Directory containing biscuit genome index
 output:
   - vcf:
       - meta:
@@ -71,3 +83,4 @@ authors:
   - "@njspix"
 maintainers:
   - "@njspix"
+  - "@sateeshperi"
diff --git a/modules/nf-core/biscuit/pileup/tests/main.nf.test b/modules/nf-core/biscuit/pileup/tests/main.nf.test
index b188103a06f..74ebff4d271 100644
--- a/modules/nf-core/biscuit/pileup/tests/main.nf.test
+++ b/modules/nf-core/biscuit/pileup/tests/main.nf.test
@@ -15,18 +15,21 @@ nextflow_process {
             script "../../index/main.nf"
             process {
                 """
-                input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
                 """
             }
         }
     }
 
-    test("homo_sapiens - test_paired_end_sorted_bam") {
+    test("homo_sapiens - paired-end [bam]") {
 
         when {
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
                     [ id:'test' ], // meta map
                     [
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
@@ -38,9 +41,12 @@ nextflow_process {
                     ],
 	                [], // tumor bam
 	                [] // tumor bai
-                ]
-
-                input[1] = BISCUIT_INDEX.out.index
+                ])
+                input[1] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -58,7 +64,7 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - test_paired_end_sorted_bam - somatic") {
+    test("homo_sapiens - paired-end [bam] - somatic") {
 
         when {
             process {
@@ -70,8 +76,11 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai', checkIfExists: true)
                 ]
-
-                input[1] = BISCUIT_INDEX.out.index
+                input[1] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -89,7 +98,7 @@ nextflow_process {
 
     }
 
-    test("homo_sapiens - test_paired_end_sorted_bam - somatic - stub") {
+    test("homo_sapiens - paired-end [bam] - somatic - stub") {
         options '-stub'
 
         when {
@@ -102,8 +111,11 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai', checkIfExists: true)
                 ]
-
-                input[1] = BISCUIT_INDEX.out.index
+                input[1] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
                 """
             }
         }
diff --git a/modules/nf-core/biscuit/pileup/tests/main.nf.test.snap b/modules/nf-core/biscuit/pileup/tests/main.nf.test.snap
index ca99df65997..14c40aa1a4d 100644
--- a/modules/nf-core/biscuit/pileup/tests/main.nf.test.snap
+++ b/modules/nf-core/biscuit/pileup/tests/main.nf.test.snap
@@ -1,31 +1,5 @@
 {
-    "homo_sapiens - test_paired_end_sorted_bam - somatic": {
-        "content": [
-            "12357b78693a704403196644b34d69a6",
-            [
-                "versions.yml:md5,d73c753b5bbc7439f06fba6c1794f719"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-29T11:43:13.955407"
-    },
-    "homo_sapiens - test_paired_end_sorted_bam": {
-        "content": [
-            "4ae9e1f5d3dbe07aca279680840bbe20",
-            [
-                "versions.yml:md5,d73c753b5bbc7439f06fba6c1794f719"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-29T11:41:00.666921"
-    },
-    "homo_sapiens - test_paired_end_sorted_bam - somatic - stub": {
+    "homo_sapiens - paired-end [bam] - somatic - stub": {
         "content": [
             {
                 "0": [
@@ -37,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d73c753b5bbc7439f06fba6c1794f719"
+                    "versions.yml:md5,beff27f24fc9327d67f5968cf1cef6cd"
                 ],
                 "vcf": [
                     [
@@ -48,14 +22,40 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d73c753b5bbc7439f06fba6c1794f719"
+                    "versions.yml:md5,beff27f24fc9327d67f5968cf1cef6cd"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T09:24:21.352967241"
+    },
+    "homo_sapiens - paired-end [bam] - somatic": {
+        "content": [
+            "5e1157703410c1a6b7cc7eded1436425",
+            [
+                "versions.yml:md5,beff27f24fc9327d67f5968cf1cef6cd"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T09:27:58.885274336"
+    },
+    "homo_sapiens - paired-end [bam]": {
+        "content": [
+            "6bea182d0b89d10246cc0ac711f6507",
+            [
+                "versions.yml:md5,beff27f24fc9327d67f5968cf1cef6cd"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-29T11:43:19.616012"
+        "timestamp": "2024-11-14T09:27:47.811858126"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/biscuit/qc/environment.yml b/modules/nf-core/biscuit/qc/environment.yml
index 56b7e967693..123215dc20f 100644
--- a/modules/nf-core/biscuit/qc/environment.yml
+++ b/modules/nf-core/biscuit/qc/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::biscuit=1.1.0.20220707
+  - bioconda::biscuit=1.5.0.20240506
diff --git a/modules/nf-core/biscuit/qc/main.nf b/modules/nf-core/biscuit/qc/main.nf
index 0ac7bd9eeab..4e63292ebd9 100644
--- a/modules/nf-core/biscuit/qc/main.nf
+++ b/modules/nf-core/biscuit/qc/main.nf
@@ -4,15 +4,16 @@ process BISCUIT_QC {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/biscuit:1.1.0.20220707--he272189_1':
-        'biocontainers/biscuit:1.1.0.20220707--he272189_1' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/33/33a9ca30b4154f11253c8d91a75382065dcb8282ba99b74dbee59ed8faceabd7/data':
+        'community.wave.seqera.io/library/biscuit:1.5.0.20240506--ca92d9d0a37b5fa8' }"
 
     input:
     tuple val(meta), path(bam)
-    path(index)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(index)
 
     output:
-    tuple val(meta), path("*.txt"), emit: biscuit_qc_reports
+    tuple val(meta), path("*.txt"), emit: reports
     path "versions.yml"           , emit: versions
 
     when:
@@ -23,12 +24,12 @@ process BISCUIT_QC {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def se = meta.single_end ? "-s" : ""
     """
-    INDEX=`find -L ./ -name "*.bis.amb" | sed 's/\\.bis.amb\$//'`
+    ln -sf \$(readlink $fasta) $index/$fasta
 
     biscuit qc \\
         $args \\
         $se \\
-        \$INDEX \\
+        $index/$fasta \\
         $bam \\
         $prefix
 
diff --git a/modules/nf-core/biscuit/qc/meta.yml b/modules/nf-core/biscuit/qc/meta.yml
index ab7500ba823..379f46bbf3e 100644
--- a/modules/nf-core/biscuit/qc/meta.yml
+++ b/modules/nf-core/biscuit/qc/meta.yml
@@ -27,11 +27,24 @@ input:
     - bam:
         type: file
         description: BAM file produced using Biscuit
-  - - index:
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
         type: file
-        description: index file
+        description: Input genome fasta file
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - index:
+        type: directory
+        description: Directory containing biscuit genome index
 output:
-  - biscuit_qc_reports:
+  - reports:
       - meta:
           type: file
           description: |
@@ -65,3 +78,4 @@ authors:
   - "@njspix"
 maintainers:
   - "@njspix"
+  - "@sateeshperi"
diff --git a/modules/nf-core/biscuit/qc/tests/main.nf.test b/modules/nf-core/biscuit/qc/tests/main.nf.test
index d4b4e57ad47..24d0dc23729 100644
--- a/modules/nf-core/biscuit/qc/tests/main.nf.test
+++ b/modules/nf-core/biscuit/qc/tests/main.nf.test
@@ -15,13 +15,16 @@ nextflow_process {
             script "../../index/main.nf"
             process {
                 """
-                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
                 """
             }
         }
     }
 
-    test("sarscov2 - test_paired_end_methylated_sorted_bam") {
+    test("sarscov2 paired-end [bam]") {
 
         when {
             process {
@@ -30,7 +33,11 @@ nextflow_process {
                     [ id:'test', single_end:false ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true)
                 ]
-                input[1] = BISCUIT_INDEX.out.index
+                input[1] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
                 """
             }
         }
@@ -44,7 +51,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - test_paired_end_methylated_sorted_bam - stub") {
+    test("sarscov2 paired-end [bam] - stub") {
         options '-stub'
 
         when {
@@ -54,7 +61,11 @@ nextflow_process {
                     [ id:'test', single_end:false ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.sorted.bam', checkIfExists: true)
                 ]
-                input[1] = BISCUIT_INDEX.out.index
+                input[1] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ])
+                input[2] = BISCUIT_INDEX.out.index
                 """
             }
         }
diff --git a/modules/nf-core/biscuit/qc/tests/main.nf.test.snap b/modules/nf-core/biscuit/qc/tests/main.nf.test.snap
index 51c995d9e5b..4c5deb3fd8d 100644
--- a/modules/nf-core/biscuit/qc/tests/main.nf.test.snap
+++ b/modules/nf-core/biscuit/qc/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "sarscov2 - test_paired_end_methylated_sorted_bam": {
+    "sarscov2 paired-end [bam]": {
         "content": [
             {
                 "0": [
@@ -20,9 +20,9 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c9bca700bf29bd9d02fc254fe070e279"
+                    "versions.yml:md5,15148723e4f43101b9e07a02566dbbd4"
                 ],
-                "biscuit_qc_reports": [
+                "reports": [
                     [
                         {
                             "id": "test",
@@ -40,17 +40,17 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c9bca700bf29bd9d02fc254fe070e279"
+                    "versions.yml:md5,15148723e4f43101b9e07a02566dbbd4"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-29T11:27:13.208945"
+        "timestamp": "2024-11-14T09:49:31.146030396"
     },
-    "sarscov2 - test_paired_end_methylated_sorted_bam - stub": {
+    "sarscov2 paired-end [bam] - stub": {
         "content": [
             {
                 "0": [
@@ -71,9 +71,9 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,c9bca700bf29bd9d02fc254fe070e279"
+                    "versions.yml:md5,15148723e4f43101b9e07a02566dbbd4"
                 ],
-                "biscuit_qc_reports": [
+                "reports": [
                     [
                         {
                             "id": "test",
@@ -91,14 +91,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c9bca700bf29bd9d02fc254fe070e279"
+                    "versions.yml:md5,15148723e4f43101b9e07a02566dbbd4"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-29T11:30:49.37928"
+        "timestamp": "2024-11-14T09:49:41.278929227"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/biscuit/vcf2bed/environment.yml b/modules/nf-core/biscuit/vcf2bed/environment.yml
index b4bab59944c..222c156ed9a 100644
--- a/modules/nf-core/biscuit/vcf2bed/environment.yml
+++ b/modules/nf-core/biscuit/vcf2bed/environment.yml
@@ -2,5 +2,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::biscuit=1.1.0.20220707
-  - bioconda::samtools=1.16.1
+  - bioconda::biscuit=1.5.0.20240506
+  - bioconda::samtools=1.21
diff --git a/modules/nf-core/biscuit/vcf2bed/main.nf b/modules/nf-core/biscuit/vcf2bed/main.nf
index f2ba512ef63..d53c8ee342b 100644
--- a/modules/nf-core/biscuit/vcf2bed/main.nf
+++ b/modules/nf-core/biscuit/vcf2bed/main.nf
@@ -4,8 +4,8 @@ process BISCUIT_VCF2BED {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-d94f582b04a3edcede1215189c0d881506640fd9:6519548ea4f3d6a526c78ad0350c58f867f28574-0':
-        'biocontainers/mulled-v2-d94f582b04a3edcede1215189c0d881506640fd9:6519548ea4f3d6a526c78ad0350c58f867f28574-0' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5b/5b542bbe1f99afd494ef07423ea8b52f2b8a081b85f92db2726c283c78da3cf0/data':
+        'community.wave.seqera.io/library/biscuit_samtools:84373c8a97fa63b8' }"
 
     input:
     tuple val(meta), path(vcf)
@@ -24,11 +24,9 @@ process BISCUIT_VCF2BED {
     """
     biscuit vcf2bed \\
         $args \\
-        $vcf | \\
-    LC_ALL=C sort -k1,1 -k2,2n | \\
-    bgzip \\
-        $args2 \\
-        -c > ${prefix}.bed.gz
+        $vcf \\
+        | LC_ALL=C sort -k1,1 -k2,2n \\
+        | bgzip $args2 -c > ${prefix}.bed.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/biscuit/vcf2bed/meta.yml b/modules/nf-core/biscuit/vcf2bed/meta.yml
index 76ee1cad11c..b50fa56d44a 100644
--- a/modules/nf-core/biscuit/vcf2bed/meta.yml
+++ b/modules/nf-core/biscuit/vcf2bed/meta.yml
@@ -48,3 +48,4 @@ authors:
   - "@njspix"
 maintainers:
   - "@njspix"
+  - "@sateeshperi"
diff --git a/modules/nf-core/biscuit/vcf2bed/tests/main.nf.test b/modules/nf-core/biscuit/vcf2bed/tests/main.nf.test
index 527f0c0ff4f..b9097a07e02 100644
--- a/modules/nf-core/biscuit/vcf2bed/tests/main.nf.test
+++ b/modules/nf-core/biscuit/vcf2bed/tests/main.nf.test
@@ -10,16 +10,15 @@ nextflow_process {
     tag "biscuit"
     tag "biscuit/vcf2bed"
 
-    test("test-biscuit-vcf2bed") {
+    test("test [vcf]") {
 
         when {
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
 				    [ id:'test', single_end:false ], // meta map
 				    file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test.vcf.gz', checkIfExists: true)
-				]
-
+				])
                 """
             }
         }
@@ -32,17 +31,16 @@ nextflow_process {
         }
     }
 
-    test("test-biscuit-vcf2bed-stub") {
+    test("test [vcf] - stub") {
         options '-stub'
 
         when {
             process {
                 """
-                input[0] = [
+                input[0] = Channel.of([
 				    [ id:'test', single_end:false ], // meta map
 				    file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/biscuit/test.vcf.gz', checkIfExists: true)
-				]
-
+				])
                 """
             }
         }
diff --git a/modules/nf-core/biscuit/vcf2bed/tests/main.nf.test.snap b/modules/nf-core/biscuit/vcf2bed/tests/main.nf.test.snap
index fd232298b85..816bd1cceaa 100644
--- a/modules/nf-core/biscuit/vcf2bed/tests/main.nf.test.snap
+++ b/modules/nf-core/biscuit/vcf2bed/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "test-biscuit-vcf2bed": {
+    "test [vcf]": {
         "content": [
             {
                 "0": [
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8626f51de333380e99cc607aaebb2cce"
+                    "versions.yml:md5,54a906013b2703ac5c5250af2a996259"
                 ],
                 "bed": [
                     [
@@ -24,17 +24,17 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8626f51de333380e99cc607aaebb2cce"
+                    "versions.yml:md5,54a906013b2703ac5c5250af2a996259"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-29T11:02:38.571195"
+        "timestamp": "2024-11-14T09:55:25.366750014"
     },
-    "test-biscuit-vcf2bed-stub": {
+    "test [vcf] - stub": {
         "content": [
             {
                 "0": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8626f51de333380e99cc607aaebb2cce"
+                    "versions.yml:md5,54a906013b2703ac5c5250af2a996259"
                 ],
                 "bed": [
                     [
@@ -59,14 +59,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8626f51de333380e99cc607aaebb2cce"
+                    "versions.yml:md5,54a906013b2703ac5c5250af2a996259"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-08-29T11:02:43.49219"
+        "timestamp": "2024-11-14T09:55:34.060320551"
     }
 }
\ No newline at end of file

From 3ef36024bb95d306c63c7bf9014132e62c7b4755 Mon Sep 17 00:00:00 2001
From: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
Date: Thu, 14 Nov 2024 16:03:39 +0200
Subject: [PATCH 03/12] clipkit - new module (#6993)

* clipkit - new module

* standard prefix.clipkit output + better meta description for the alignment file
---
 modules/nf-core/clipkit/environment.yml       |  7 ++
 modules/nf-core/clipkit/main.nf               | 46 +++++++++++++
 modules/nf-core/clipkit/meta.yml              | 50 ++++++++++++++
 modules/nf-core/clipkit/tests/main.nf.test    | 66 ++++++++++++++++++
 .../nf-core/clipkit/tests/main.nf.test.snap   | 68 +++++++++++++++++++
 5 files changed, 237 insertions(+)
 create mode 100644 modules/nf-core/clipkit/environment.yml
 create mode 100644 modules/nf-core/clipkit/main.nf
 create mode 100644 modules/nf-core/clipkit/meta.yml
 create mode 100644 modules/nf-core/clipkit/tests/main.nf.test
 create mode 100644 modules/nf-core/clipkit/tests/main.nf.test.snap

diff --git a/modules/nf-core/clipkit/environment.yml b/modules/nf-core/clipkit/environment.yml
new file mode 100644
index 00000000000..65c451ffb1f
--- /dev/null
+++ b/modules/nf-core/clipkit/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::clipkit=2.3.0"
diff --git a/modules/nf-core/clipkit/main.nf b/modules/nf-core/clipkit/main.nf
new file mode 100644
index 00000000000..2a9ebe3f851
--- /dev/null
+++ b/modules/nf-core/clipkit/main.nf
@@ -0,0 +1,46 @@
+process CLIPKIT {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/clipkit:2.3.0--pyhdfd78af_0':
+        'biocontainers/clipkit:2.3.0--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(aln)
+
+    output:
+    tuple val(meta), path("*.clipkit"), emit: clipkit
+    path "versions.yml"               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    clipkit \\
+        $args \\
+        $aln \\
+        -o ${prefix}.clipkit
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        clipkit: \$(clipkit --version |& sed '1!d ; s/clipkit //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.clipkit
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        clipkit: \$(clipkit --version |& sed '1!d ; s/clipkit //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/clipkit/meta.yml b/modules/nf-core/clipkit/meta.yml
new file mode 100644
index 00000000000..5347ad5923a
--- /dev/null
+++ b/modules/nf-core/clipkit/meta.yml
@@ -0,0 +1,50 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "clipkit"
+description: ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes those that display characteristics poor phylogenetic signal.
+keywords:
+  - sort
+  - example
+  - genomics
+tools:
+  - "clipkit":
+      description: "Alignment trimming software for phylogenetics."
+      homepage: "https://jlsteenwyk.com/ClipKIT/"
+      documentation: "https://jlsteenwyk.com/ClipKIT/"
+      tool_dev_url: "https://github.com/JLSteenwyk/ClipKIT"
+      doi: "10.1371/journal.pbio.3001007"
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - aln:
+        type: file
+        description: Multiple sequence alignment file in various supported formats.
+        pattern: "*.{fa,fasta,fa,fna,faa,alnfaa,aln,sto,stk,mauve,alignment,clustal}"
+
+output:
+  - clipkit:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.clipkit":
+          type: file
+          description: Trimmed multiple sequence alignment file
+          pattern: "*.clipkit"
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@vagkaratzas"
+maintainers:
+  - "@vagkaratzas"
diff --git a/modules/nf-core/clipkit/tests/main.nf.test b/modules/nf-core/clipkit/tests/main.nf.test
new file mode 100644
index 00000000000..46cc8a00716
--- /dev/null
+++ b/modules/nf-core/clipkit/tests/main.nf.test
@@ -0,0 +1,66 @@
+nextflow_process {
+
+    name "Test Process CLIPKIT"
+    script "../main.nf"
+    process "CLIPKIT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "clipkit"
+    tag "gunzip"
+
+    setup {
+        run("GUNZIP") {
+            script "../../gunzip/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'PF14720' ], // meta map
+                    file(params.modules_testdata_base_path + 'delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("PF14720 - aln") {
+
+        when {
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("PF14720 - aln - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/clipkit/tests/main.nf.test.snap b/modules/nf-core/clipkit/tests/main.nf.test.snap
new file mode 100644
index 00000000000..55f837d9e52
--- /dev/null
+++ b/modules/nf-core/clipkit/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "PF14720 - aln - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "PF14720"
+                        },
+                        "PF14720.clipkit:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1eaf2dc589bc08c1e37cbbddbedfcc80"
+                ],
+                "clipkit": [
+                    [
+                        {
+                            "id": "PF14720"
+                        },
+                        "PF14720.clipkit:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1eaf2dc589bc08c1e37cbbddbedfcc80"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
+        },
+        "timestamp": "2024-11-14T13:11:21.109400968"
+    },
+    "PF14720 - aln": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "PF14720"
+                        },
+                        "PF14720.clipkit:md5,97e4328b5990f5e5a6241c225ed6d922"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,1eaf2dc589bc08c1e37cbbddbedfcc80"
+                ],
+                "clipkit": [
+                    [
+                        {
+                            "id": "PF14720"
+                        },
+                        "PF14720.clipkit:md5,97e4328b5990f5e5a6241c225ed6d922"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,1eaf2dc589bc08c1e37cbbddbedfcc80"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "23.04.5"
+        },
+        "timestamp": "2024-11-14T13:11:14.278212183"
+    }
+}
\ No newline at end of file

From 0e2d0c6d94f048eb1ba88924a0c87edc2c1bd6ef Mon Sep 17 00:00:00 2001
From: Edmund Miller <20095261+edmundmiller@users.noreply.github.com>
Date: Thu, 14 Nov 2024 09:25:15 -0600
Subject: [PATCH 04/12] Wave with Dockerfiles (#4940)

* ci(renovate): Add Dockerfile building

* build: Bump quarto to 24.04

* ci: Get clever with singularity flag

* build: Try a better Dockerfile

* ci(wave): Better names

* ci(wave): Properly skip environment.yml and Dockerfiles

* style(wittyer): Remove environment.yml

* ci(wave): Let Dockerfiles fail and request @edmundmiller and @maxulysse
---
 .github/CODEOWNERS                        |   1 +
 .github/workflows/wave.yml                | 101 ++++++++++++++--------
 modules/nf-core/quartonotebook/Dockerfile |   2 +-
 modules/nf-core/wittyer/Dockerfile        |   2 +
 modules/nf-core/wittyer/environment.yml   |   5 --
 5 files changed, 71 insertions(+), 40 deletions(-)
 delete mode 100644 modules/nf-core/wittyer/environment.yml

diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
index 3893bf75737..9552f7c99ad 100644
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@@ -12,3 +12,4 @@ modules/nf-core/pints/caller/** @edmundmiller
 modules/nf-core/preseq/ccurve/** @edmundmiller
 modules/nf-core/preseq/lcextrap/** @edmundmiller
 subworkflows/nf-core/homer/** @edmundmiller
+modules/nf-core/**/Dockerfile @edmundmiller @maxulysse
diff --git a/.github/workflows/wave.yml b/.github/workflows/wave.yml
index 4f36575b6d1..a86fd9bb10a 100644
--- a/.github/workflows/wave.yml
+++ b/.github/workflows/wave.yml
@@ -4,6 +4,7 @@ on:
   pull_request:
     paths:
       - "**/environment.yml"
+      - "**/Dockerfile"
 
 # TODO On complete call testing CI
 # TODO Skip testing CI if any changes to environment.yml
@@ -18,38 +19,44 @@ jobs:
     runs-on: ubuntu-latest
     # Only run on Pull Requests within the same repository, and not from forks
     if: github.event.pull_request.head.repo.full_name == github.repository
-
+    outputs:
+      conda-matrix: ${{ steps.conda-diff.outputs.all_changed_files }}
+      docker-matrix: ${{ steps.docker-diff.outputs.all_changed_files }}
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Calculate file differences
-        id: diff
+      - name: Find conda differences
+        id: conda-diff
         uses: tj-actions/changed-files@4edd678ac3f81e2dc578756871e4d00c19191daf # v45
         with:
           json: true
-          quotepath: false
-          # TODO Add Dockerfiles
+          escape_json: false
           files: |
             modules/**/environment.yml
-      - name: Debug
-        run: echo ${{ steps.diff.outputs.all_changed_files }}
-      - id: set-matrix
-        run: echo "matrix={\"profile\":[\"docker\", \"singularity\"],\"files\":${{ steps.diff.outputs.all_changed_files }} }" >> "$GITHUB_OUTPUT"
 
-    outputs:
-      matrix: ${{ steps.set-matrix.outputs.matrix }}
+      - name: Find Dockerfile differences
+        id: docker-diff
+        uses: tj-actions/changed-files@4edd678ac3f81e2dc578756871e4d00c19191daf # v45
+        with:
+          json: true
+          escape_json: false
+          files: |
+            modules/**/Dockerfile
 
-  build:
+  conda-wave:
     # NOTE This should get skipped because generate-matrix won't run
     # if: github.repository == 'nf-core/modules'
-    if: "${{ fromJson(needs.generate-matrix.outputs.matrix) }}"
+    if: ${{ needs.generate-matrix.outputs.conda-matrix != '[]' }}
     needs: generate-matrix
-    name: build
+    name: Build Conda-based ${{ matrix.profile }} Container
     runs-on: ubuntu-latest
     timeout-minutes: 60
     strategy:
       fail-fast: false
-      matrix: "${{ fromJson(needs.generate-matrix.outputs.matrix) }}"
+      max-parallel: 4
+      matrix:
+        files: "${{ fromJson(needs.generate-matrix.outputs.conda-matrix) }}"
+        profile: [docker, singularity]
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
@@ -59,38 +66,64 @@ jobs:
           sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave
           chmod +x /usr/local/bin/wave
 
-      - name: Create a registry name
-        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
-        id: registry-name
-        with:
-          result-encoding: string
-          script: |
-            return '${{ matrix.files }}'.replace('modules/nf-core/', '').replace('/environment.yml', '').replace('/', '_');
-
-      - name: Build container
+      - name: Build ${{ matrix.profile }} container
         # FIXME Hack while iron out the CI
         continue-on-error: true
-        if: matrix.profile == 'docker'
+        env:
+          PROFILE: ${{ (contains(matrix.profile, 'singularity') && '--singularity') || '' }}
         run: |
           wave --conda-file "${{ matrix.files }}" \
+              $PROFILE \
               --freeze \
               --await \
               --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
               --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}
 
-      - name: Build Singularity
-        # FIXME Hack while iron out the CI
-        continue-on-error: true
-        if: matrix.profile == 'singularity'
+  docker-wave:
+    # NOTE This should get skipped because generate-matrix won't run
+    # if: github.repository == 'nf-core/modules'
+    if: ${{ needs.generate-matrix.outputs.docker-matrix != '[]' }}
+    needs: generate-matrix
+    name: Build Dockerfile-based ${{ matrix.profile }} Container
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      max-parallel: 4
+      matrix:
+        files: "${{ fromJson(needs.generate-matrix.outputs.docker-matrix) }}"
+        profile: [docker, singularity]
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+
+      - name: Install wave-cli
         run: |
-          wave --conda-file "${{ matrix.files }}" \
+          wget -q https://github.com/seqeralabs/wave-cli/releases/download/v${WAVE_VER}/wave-${WAVE_VER}-linux-x86_64
+          sudo mv wave-${WAVE_VER}-linux-x86_64 /usr/local/bin/wave
+          chmod +x /usr/local/bin/wave
+
+      - name: Create a registry name
+        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
+        id: registry-name
+        with:
+          result-encoding: string
+          script: |
+            return '${{ matrix.files }}'.replace('modules/nf-core/', '').replace('/Dockerfile', '').replace('/', '_');
+
+      - name: Build ${{ matrix.profile }} container
+        # NOTE If you're changing a Dockerfile and this is running, try to update the Dockerfile to build with wave
+        continue-on-error: false
+        env:
+          PROFILE: ${{ (contains(matrix.profile, 'singularity') && '--singularity') || '' }}
+        run: |
+          wave -f "${{ matrix.files }}" \
+              $PROFILE \
               --freeze \
               --await \
+              --build-repo quay.io/nf-core/modules/${{steps.registry-name.outputs.result}} \
+              --cache-repository quay.io/nf-core/wave-cache \
               --tower-token ${{ secrets.TOWER_ACCESS_TOKEN }} \
-              --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }} \
-              --singularity
-
-    # TODO Build from Dockerfiles
+              --tower-workspace-id ${{ secrets.TOWER_WORKSPACE_ID }}
 
   # bump-versions:
   #   needs: generate-matrix
diff --git a/modules/nf-core/quartonotebook/Dockerfile b/modules/nf-core/quartonotebook/Dockerfile
index 78d2ab20c23..26624b7ea6d 100644
--- a/modules/nf-core/quartonotebook/Dockerfile
+++ b/modules/nf-core/quartonotebook/Dockerfile
@@ -1,7 +1,7 @@
 #
 # First stage: Quarto installation
 #
-FROM ubuntu:20.04 as quarto
+FROM ubuntu:24.04 as quarto
 ARG QUARTO_VERSION=1.3.433
 ARG TARGETARCH
 RUN apt-get update \
diff --git a/modules/nf-core/wittyer/Dockerfile b/modules/nf-core/wittyer/Dockerfile
index fae697ab9dc..fbf732f32bd 100644
--- a/modules/nf-core/wittyer/Dockerfile
+++ b/modules/nf-core/wittyer/Dockerfile
@@ -1,4 +1,5 @@
 FROM mcr.microsoft.com/dotnet/sdk:6.0@sha256:6df1177e48b55272316d08f19cb383483af82aca5cdc67a76c414bc200847624 as builder
+
 WORKDIR /src
 COPY . /src
 RUN cd Wittyer \
@@ -6,6 +7,7 @@ RUN cd Wittyer \
     && chmod +x /output/Wittyer
 
 FROM mcr.microsoft.com/dotnet/runtime:6.0@sha256:437cda84bdce26ce074d88b63abeec567c7226d73e8b911605077468e1d5c8d5
+
 LABEL git_repository=https://git.illumina.com/DASTE/Ilmn.Das.App.Wittyer.git
 WORKDIR /opt/Wittyer
 RUN apt-get -y update && apt-get -y install tabix libunwind8 openssl procps
diff --git a/modules/nf-core/wittyer/environment.yml b/modules/nf-core/wittyer/environment.yml
deleted file mode 100644
index c90cb8dccbf..00000000000
--- a/modules/nf-core/wittyer/environment.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-channels:
-  - conda-forge
-  - bioconda
-dependencies:
-  - tabix

From 754825005d1c009e0221aca276aeabf1972ca31b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kre=C5=A1imir=20Be=C5=A1tak?=
 <86408271+kbestak@users.noreply.github.com>
Date: Thu, 14 Nov 2024 23:54:32 +0100
Subject: [PATCH 05/12] nf-test for ashlar (#6931)

* nf-test for ashlar

* Update modules/nf-core/ashlar/main.nf

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>

* added multiple tests

* pin tifffile version

---------

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/nf-core/ashlar/environment.yml        |   1 +
 modules/nf-core/ashlar/main.nf                |  20 +++
 modules/nf-core/ashlar/tests/main.nf.test     | 155 ++++++++++++++++
 .../nf-core/ashlar/tests/main.nf.test.snap    | 167 ++++++++++++++++++
 modules/nf-core/ashlar/tests/nextflow.config  |   5 +
 tests/config/pytest_modules.yml               |   3 -
 tests/modules/nf-core/ashlar/main.nf          |  90 ----------
 tests/modules/nf-core/ashlar/nextflow.config  |   9 -
 tests/modules/nf-core/ashlar/test.yml         |  44 -----
 9 files changed, 348 insertions(+), 146 deletions(-)
 create mode 100644 modules/nf-core/ashlar/tests/main.nf.test
 create mode 100644 modules/nf-core/ashlar/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/ashlar/tests/nextflow.config
 delete mode 100644 tests/modules/nf-core/ashlar/main.nf
 delete mode 100644 tests/modules/nf-core/ashlar/nextflow.config
 delete mode 100644 tests/modules/nf-core/ashlar/test.yml

diff --git a/modules/nf-core/ashlar/environment.yml b/modules/nf-core/ashlar/environment.yml
index 8b3e771ac01..502f7177299 100644
--- a/modules/nf-core/ashlar/environment.yml
+++ b/modules/nf-core/ashlar/environment.yml
@@ -3,3 +3,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::ashlar=1.18.0
+  - tifffile=2024.1.30
diff --git a/modules/nf-core/ashlar/main.nf b/modules/nf-core/ashlar/main.nf
index 2ddc710feb5..86120b8de58 100644
--- a/modules/nf-core/ashlar/main.nf
+++ b/modules/nf-core/ashlar/main.nf
@@ -49,4 +49,24 @@ process ASHLAR {
         ashlar: \$(ashlar --version | sed 's/^.*ashlar //' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix        = task.ext.prefix         ?: "${meta.id}"
+    def num_files     = images instanceof List  ? images.size()    : 1
+    def opt_dfp_size  = opt_dfp instanceof List ? opt_dfp.size()   : 1
+    def opt_ffp_size  = opt_ffp instanceof List ? opt_ffp.size()   : 1
+    def dfp_validated = (opt_dfp_size == 0 || opt_dfp_size == 1 || opt_dfp_size == num_files) ? true : false
+    def ffp_validated = (opt_ffp_size == 0 || opt_ffp_size == 1 || opt_ffp_size == num_files) ? true : false
+
+    if ( !dfp_validated ) { error "Please input only zero, one, or N dfp files, where N is the number of input images" }
+    if ( !ffp_validated ) { error "Please input only zero, one, or N ffp files, where N is the number of input images" }
+
+    """
+    touch ${prefix}.ome.tif
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ashlar: \$(ashlar --version | sed 's/^.*ashlar //' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/ashlar/tests/main.nf.test b/modules/nf-core/ashlar/tests/main.nf.test
new file mode 100644
index 00000000000..fd69ebd500d
--- /dev/null
+++ b/modules/nf-core/ashlar/tests/main.nf.test
@@ -0,0 +1,155 @@
+nextflow_process {
+
+    name "Test Process ASHLAR"
+    script "../main.nf"
+    process "ASHLAR"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ashlar"
+
+    test("ashlar - with fields") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test_all' ],
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true)
+                ]
+                input[1] = [
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-dfp.ome.tif', checkIfExists: true)
+                ]
+                input[2] = [
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-ffp.ome.tif', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("ashlar - 1 cycle - ome-tif") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test_1' ],
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true)
+                ]
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("ashlar - all cycles - ome-tif") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test_1' ],
+                                [
+                                    file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true),
+                                    file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif', checkIfExists: true),
+                                    file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif', checkIfExists: true)
+
+                                ]
+                ]
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("ashlar - all cycles - with fields - ome-tif") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test_1' ],
+                                [
+                                    file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true),
+                                    file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle2.ome.tif', checkIfExists: true),
+                                    file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle3.ome.tif', checkIfExists: true)
+
+                                ]
+                ]
+                input[1] = [
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-dfp.ome.tif', checkIfExists: true)
+                ]
+                input[2] = [
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-ffp.ome.tif', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("ashlar - with fields - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test_all' ],
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true)
+                ]
+                input[1] = [
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-dfp.ome.tif', checkIfExists: true)
+                ]
+                input[2] = [
+                                file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-ffp.ome.tif', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/ashlar/tests/main.nf.test.snap b/modules/nf-core/ashlar/tests/main.nf.test.snap
new file mode 100644
index 00000000000..7c41f5b6d3e
--- /dev/null
+++ b/modules/nf-core/ashlar/tests/main.nf.test.snap
@@ -0,0 +1,167 @@
+{
+    "ashlar - with fields - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_all"
+                        },
+                        "test_all.ome.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ],
+                "tif": [
+                    [
+                        {
+                            "id": "test_all"
+                        },
+                        "test_all.ome.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-04T13:32:44.241620025"
+    },
+    "ashlar - 1 cycle - ome-tif": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_1"
+                        },
+                        "test_1.ome.tif:md5,988bbb2c74d47dc22a9f3ac348f53ef5"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ],
+                "tif": [
+                    [
+                        {
+                            "id": "test_1"
+                        },
+                        "test_1.ome.tif:md5,988bbb2c74d47dc22a9f3ac348f53ef5"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-06T11:13:49.614970275"
+    },
+    "ashlar - with fields": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_all"
+                        },
+                        "test_all.ome.tif:md5,988bbb2c74d47dc22a9f3ac348f53ef5"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ],
+                "tif": [
+                    [
+                        {
+                            "id": "test_all"
+                        },
+                        "test_all.ome.tif:md5,988bbb2c74d47dc22a9f3ac348f53ef5"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-04T13:28:26.923837754"
+    },
+    "ashlar - all cycles - ome-tif": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_1"
+                        },
+                        "test_1.ome.tif:md5,c01dda923325588ea34a4fe341b17e6e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ],
+                "tif": [
+                    [
+                        {
+                            "id": "test_1"
+                        },
+                        "test_1.ome.tif:md5,c01dda923325588ea34a4fe341b17e6e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-06T11:14:14.530220621"
+    },
+    "ashlar - all cycles - with fields - ome-tif": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_1"
+                        },
+                        "test_1.ome.tif:md5,c01dda923325588ea34a4fe341b17e6e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ],
+                "tif": [
+                    [
+                        {
+                            "id": "test_1"
+                        },
+                        "test_1.ome.tif:md5,c01dda923325588ea34a4fe341b17e6e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,d5b1baeee01093ff65d37e155c9ce462"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-06T11:14:56.268009236"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/ashlar/tests/nextflow.config b/modules/nf-core/ashlar/tests/nextflow.config
new file mode 100644
index 00000000000..f7f07fcb6fb
--- /dev/null
+++ b/modules/nf-core/ashlar/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: ASHLAR_TILE {
+        ext.args = "--tile-size 512"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 2e0e6420c33..887e215cbe8 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -22,9 +22,6 @@ artic/minion:
 ascat:
   - modules/nf-core/ascat/**
   - tests/modules/nf-core/ascat/**
-ashlar:
-  - modules/nf-core/ashlar/**
-  - tests/modules/nf-core/ashlar/**
 ataqv/ataqv:
   - modules/nf-core/ataqv/ataqv/**
   - tests/modules/nf-core/ataqv/ataqv/**
diff --git a/tests/modules/nf-core/ashlar/main.nf b/tests/modules/nf-core/ashlar/main.nf
deleted file mode 100644
index 278bc3195c7..00000000000
--- a/tests/modules/nf-core/ashlar/main.nf
+++ /dev/null
@@ -1,90 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { ASHLAR } from '../../../../modules/nf-core/ashlar/main.nf'
-include { ASHLAR as ASHLAR_TILE } from '../../../../modules/nf-core/ashlar/main.nf'
-
-workflow test_ashlar_1_file {
-
-    input_list =  [ [ id:'test_all' ],
-               [file(params.test_data['imaging']
-                                     ['ome-tiff']
-                                     ['cycif_tonsil_cycle1'], checkIfExists: true)] ]
-
-    ASHLAR ( input_list, [], [] )
-
-}
-
-workflow test_ashlar_all_files {
-
-    input_list =  [ [ id:'test_all' ],
-               [file(params.test_data['imaging']
-                                     ['ome-tiff']
-                                     ['cycif_tonsil_cycle1'], checkIfExists: true),
-                file(params.test_data['imaging']
-                                     ['ome-tiff']
-                                     ['cycif_tonsil_cycle2'], checkIfExists: true),
-                file(params.test_data['imaging']
-                                     ['ome-tiff']
-                                     ['cycif_tonsil_cycle3'], checkIfExists: true)] ]
-
-    ASHLAR ( input_list, [], [] )
-
-}
-
-workflow test_ashlar_all_files_tile_size {
-
-    input_list =  [ [ id:'test_all' ],
-               [file(params.test_data['imaging']
-                                     ['ome-tiff']
-                                     ['cycif_tonsil_cycle1'], checkIfExists: true),
-                file(params.test_data['imaging']
-                                     ['ome-tiff']
-                                     ['cycif_tonsil_cycle2'], checkIfExists: true),
-                file(params.test_data['imaging']
-                                     ['ome-tiff']
-                                     ['cycif_tonsil_cycle3'], checkIfExists: true)] ]
-
-    ASHLAR_TILE ( input_list, [], [] )
-
-}
-
-workflow test_ashlar_all_files_dfp_ffp {
-
-    input_list =  [ [ id:'test_all' ],
-               [file(params.test_data['imaging']
-                                     ['ome-tiff']
-                                     ['cycif_tonsil_cycle1'], checkIfExists: true),
-                file(params.test_data['imaging']
-                                     ['ome-tiff']
-                                     ['cycif_tonsil_cycle2'], checkIfExists: true),
-                file(params.test_data['imaging']
-                                     ['ome-tiff']
-                                     ['cycif_tonsil_cycle3'], checkIfExists: true)] ]
-
-    ASHLAR ( input_list, [file(params.test_data['imaging']
-                                               ['ome-tiff']
-                                               ['cycif_tonsil_dfp'], checkIfExists: true)],
-                         [file(params.test_data['imaging']
-                                               ['ome-tiff']
-                                               ['cycif_tonsil_ffp'], checkIfExists: true)] )
-
-}
-
-workflow test_ashlar_1_file_dfp_ffp {
-
-    input_list =  [ [ id:'test_all' ],
-               [file(params.test_data['imaging']
-                                     ['ome-tiff']
-                                     ['cycif_tonsil_cycle1'], checkIfExists: true)] ]
-
-    ASHLAR ( input_list, [file(params.test_data['imaging']
-                                               ['ome-tiff']
-                                               ['cycif_tonsil_dfp'], checkIfExists: true)],
-                         [file(params.test_data['imaging']
-                                               ['ome-tiff']
-                                               ['cycif_tonsil_ffp'], checkIfExists: true)] )
-
-}
-
diff --git a/tests/modules/nf-core/ashlar/nextflow.config b/tests/modules/nf-core/ashlar/nextflow.config
deleted file mode 100644
index 9b566dd3953..00000000000
--- a/tests/modules/nf-core/ashlar/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName: ASHLAR_TILE {
-        ext.args = "--tile-size 512"
-    }
-
-}
diff --git a/tests/modules/nf-core/ashlar/test.yml b/tests/modules/nf-core/ashlar/test.yml
deleted file mode 100644
index 0dad0fdd990..00000000000
--- a/tests/modules/nf-core/ashlar/test.yml
+++ /dev/null
@@ -1,44 +0,0 @@
-- name: ashlar test_ashlar_1_file
-  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_1_file -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
-  tags:
-    - ashlar
-  files:
-    - path: output/ashlar/test_all.ome.tif
-      md5sum: 988bbb2c74d47dc22a9f3ac348f53ef5
-    - path: output/ashlar/versions.yml
-
-- name: ashlar test_ashlar_all_files
-  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
-  tags:
-    - ashlar
-  files:
-    - path: output/ashlar/test_all.ome.tif
-      md5sum: c01dda923325588ea34a4fe341b17e6e
-    - path: output/ashlar/versions.yml
-
-- name: ashlar test_ashlar_all_files_tile_size
-  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_tile_size -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
-  tags:
-    - ashlar
-  files:
-    - path: output/ashlar/test_all.ome.tif
-      md5sum: 6d9573d40a93e38356ebc8b257f8dfb9
-    - path: output/ashlar/versions.yml
-
-- name: ashlar test_ashlar_all_files_dfp_ffp
-  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_all_files_dfp_ffp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
-  tags:
-    - ashlar
-  files:
-    - path: output/ashlar/test_all.ome.tif
-      md5sum: c01dda923325588ea34a4fe341b17e6e
-    - path: output/ashlar/versions.yml
-
-- name: ashlar test_ashlar_1_file_dfp_ffp
-  command: nextflow run ./tests/modules/nf-core/ashlar -entry test_ashlar_1_file_dfp_ffp -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ashlar/nextflow.config
-  tags:
-    - ashlar
-  files:
-    - path: output/ashlar/test_all.ome.tif
-      md5sum: 988bbb2c74d47dc22a9f3ac348f53ef5
-    - path: output/ashlar/versions.yml

From 4a76db98b110df9f802cb6436019427b2d336368 Mon Sep 17 00:00:00 2001
From: Takeshi Gitano <gitanoqevaporelmundoentero@gmail.com>
Date: Fri, 15 Nov 2024 15:08:25 +0100
Subject: [PATCH 06/12] parabricks/applybqsr version updated and tests migrated
 to nf-test (#6881)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* parabricks/applybqsr version updated and tests migrated to pytest

* parabricks/applybqsr version updated and tests migrated to pytest

* modules update & possibly anything more

* modules update & possibly anything more

* modules update & possibly anything more

* modules update & possibly anything more

* parabricks/applybqsr version updated and tests migrated to pytest

* update snaps

* parabricks/applybqsr version updated and tests migrated to pytest

* parabricks/applybqsr version updated and tests migrated to pytest

* new snap

* parabricks/applybqsr version updated and tests migrated to pytest

* parabricks/applybqsr version updated and tests migrated to pytest

* parabricks/applybqsr version updated and tests migrated to pytest

* update snap

* parabricks/applybqsr version updated and tests migrated to pytest

* parabricks/applybqsr version updated and tests migrated to pytest

* update snap

* parabricks/applybqsr version updated and tests migrated to pytest

* parabricks/applybqsr version updated and tests migrated to pytest

* add other parabricks modules

* add gpu label

* remove old txt file

* remove parabricks from normal nf-test

* exclude parabricks from conda

* fix excluding

* simplify excluding

* add docker debugging step

* more debbuging

* more debugging

* add ssh step

* move ssh debugging

* remove ssh debugging

* fix debugging step

* add ssh-tunnel back

* remove debugging

* add gpu profile to test

* modify test inclusion

* update fq2bam snap

* update snap fq2bammeth

* remove fq2bammeth

---------

Co-authored-by: orodrig3 <oscar.rodriguez-cruz@t-systems.com>
Co-authored-by: famosab <famke.baeuerle@gmail.com>
Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu3@gmail.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 .github/workflows/test.yml                    | 144 ++++++++++--
 .../parabricks/applybqsr/environment.yml      |   3 -
 modules/nf-core/parabricks/applybqsr/main.nf  |  13 +-
 modules/nf-core/parabricks/applybqsr/meta.yml |  17 +-
 .../parabricks/applybqsr/tests/main.nf.test   | 213 ++++++++++++++++++
 .../applybqsr/tests/main.nf.test.snap         | 142 ++++++++++++
 modules/nf-core/parabricks/fq2bam/main.nf     |   1 +
 .../parabricks/fq2bam/tests/main.nf.test.snap |  20 +-
 .../fq2bammeth/tests/main.nf.test.snap        |  36 ++-
 tests/config/nextflow.config                  |   5 +
 tests/config/nf-test.config                   |   6 +
 tests/config/pytest_modules.yml               |   3 -
 .../nf-core/parabricks/applybqsr/main.nf      |  39 ----
 .../parabricks/applybqsr/nextflow.config      |   5 -
 .../nf-core/parabricks/applybqsr/test.yml     |  21 --
 .../parabricks/applybqsr/test_GPU_config.txt  |   9 -
 16 files changed, 544 insertions(+), 133 deletions(-)
 delete mode 100644 modules/nf-core/parabricks/applybqsr/environment.yml
 create mode 100644 modules/nf-core/parabricks/applybqsr/tests/main.nf.test
 create mode 100644 modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap
 delete mode 100644 tests/modules/nf-core/parabricks/applybqsr/main.nf
 delete mode 100644 tests/modules/nf-core/parabricks/applybqsr/nextflow.config
 delete mode 100644 tests/modules/nf-core/parabricks/applybqsr/test.yml
 delete mode 100644 tests/modules/nf-core/parabricks/applybqsr/test_GPU_config.txt

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 43fe9733d3a..4c22ed82bed 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -344,14 +344,10 @@ jobs:
             tags: nanoplot
           - profile: conda
             tags: ncbitools/vecscreen
-          - profile: conda
-            tags: parabricks/applybqsr
           - profile: conda
             tags: parabricks/dbsnp
           - profile: conda
             tags: parabricks/deepvariant
-          - profile: conda
-            tags: parabricks/fq2bam
           - profile: conda
             tags: parabricks/genotypegvcf
           - profile: conda
@@ -648,18 +644,6 @@ jobs:
             path: modules/nf-core/islandpath
           - profile: conda
             path: modules/nf-core/scimap/mcmicro
-          - profile: conda
-            path: modules/nf-core/parabricks/fq2bammeth
-          - profile: docker_self_hosted
-            path: modules/nf-core/parabricks/fq2bammeth
-          - profile: singularity
-            path: modules/nf-core/parabricks/fq2bammeth
-          - profile: conda
-            path: modules/nf-core/parabricks/fq2bam
-          - profile: docker_self_hosted
-            path: modules/nf-core/parabricks/fq2bam
-          - profile: singularity
-            path: modules/nf-core/parabricks/fq2bam
           - profile: conda
             path: subworkflows/nf-core/vcf_annotate_ensemblvep
           - profile: conda
@@ -672,6 +656,9 @@ jobs:
             path: subworkflows/nf-core/fastq_align_bwa
           - profile: conda
             path: subworkflows/nf-core/fasta_newick_epang_gappa
+          - path: modules/nf-core/parabricks/fq2bammeth
+          - path: modules/nf-core/parabricks/fq2bam
+          - path: modules/nf-core/parabricks/applybqsr
           - profile: conda
             path: modules/nf-core/xeniumranger/relabel
           - profile: conda
@@ -786,6 +773,131 @@ jobs:
         run: |
           sudo rm -rf /home/ubuntu/tests/
 
+  nf-test-gpu:
+    runs-on: ${{ github.event.inputs.runners  || 'gpu' }}
+    name: nf-test with GPUs
+    needs: [nf-test-changes]
+    if: ( needs.nf-test-changes.outputs.paths != '[]' )
+    strategy:
+      fail-fast: false
+      matrix:
+        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
+        profile: [conda, docker_self_hosted, singularity]
+        include:
+          - path: modules/nf-core/parabricks/applybqsr
+          - path: modules/nf-core/parabricks/fq2bam
+          # - path: modules/nf-core/parabricks/fq2bammeth excluded - tackle in different PR
+        exclude:
+          - profile: conda
+            path: modules/nf-core/parabricks/fq2bam
+          - profile: conda
+            path: modules/nf-core/parabricks/fq2bammeth
+          - profile: conda
+            path: modules/nf-core/parabricks/applybqsr
+    env:
+      NXF_ANSI_LOG: false
+      NFTEST_VER: "0.9.0"
+      SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
+      SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
+
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+
+      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v2
+
+      - name: Install nf-test
+        uses: nf-core/setup-nf-test@v1
+        with:
+          version: ${{ env.NFTEST_VER }}
+
+      - name: Setup apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        run: |
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up Python
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        with:
+          python-version: "3.11"
+
+      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
+        id: cache-pip-pdiff
+        with:
+          path: ~/.cache/pip
+          key: ${{ runner.os }}-pip-pdiff
+          restore-keys: |
+            ${{ runner.os }}-pip-pdiff
+
+      - name: Install Python dependencies
+        run: python -m pip install --upgrade pip pdiff cryptography
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          channels: conda-forge,bioconda
+
+      - name: Conda setup
+        if: matrix.profile == 'conda'
+        run: |
+          conda clean -a
+          conda install -n base conda-libmamba-solver
+          conda config --set solver libmamba
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      # Set up secrets
+      - name: Set up nextflow secrets
+        # TODO Only run if the tag includes `sentieon`
+        if: env.SENTIEON_ENCRYPTION_KEY != null && env.SENTIEON_LICENSE_MESSAGE != null
+        run: |
+          nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "${{ secrets.SENTIEON_LICENSE_MESSAGE }}")
+      # Test the module
+      - name: Run nf-test
+        if: ${{ matrix.path != '' }}
+        env:
+          NFT_DIFF: "pdiff"
+          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
+          SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
+          SENTIEON_AUTH_MECH: "GitHub Actions - token"
+        run: |
+          # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker
+          if [ "${{ matrix.profile }}" == "docker" ]; then
+            PROFILE="docker_self_hosted"
+          else
+            PROFILE=${{ matrix.profile }}
+          fi
+
+          NFT_WORKDIR=~ \
+          nf-test test \
+            --profile=${{ matrix.profile }},gpu \
+            --tap=test.tap \
+            --verbose \
+            ${{ matrix.path }}
+
+      - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
+        if: ${{ matrix.path != '' }}
+        with:
+          path: >-
+            test.tap
+
+      - name: Clean up
+        if: always()
+        run: |
+          sudo rm -rf /home/ubuntu/tests/
+
   confirm-pass:
     runs-on: ubuntu-latest
     needs:
diff --git a/modules/nf-core/parabricks/applybqsr/environment.yml b/modules/nf-core/parabricks/applybqsr/environment.yml
deleted file mode 100644
index 3cebeff05bf..00000000000
--- a/modules/nf-core/parabricks/applybqsr/environment.yml
+++ /dev/null
@@ -1,3 +0,0 @@
-channels:
-  - conda-forge
-  - bioconda
diff --git a/modules/nf-core/parabricks/applybqsr/main.nf b/modules/nf-core/parabricks/applybqsr/main.nf
index b545297d89a..38b2af002b8 100644
--- a/modules/nf-core/parabricks/applybqsr/main.nf
+++ b/modules/nf-core/parabricks/applybqsr/main.nf
@@ -1,12 +1,16 @@
 process PARABRICKS_APPLYBQSR {
     tag "$meta.id"
     label 'process_high'
+    label 'process_gpu'
 
-    container "nvcr.io/nvidia/clara/clara-parabricks:4.3.0-1"
+    container "nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1"
 
     input:
-    tuple val(meta), path(bam), path(bam_index), path(bqsr_table), path(intervals)
-    tuple val(meta2), path(fasta)
+    tuple val(meta), path(bam)
+    tuple val(meta2), path(bam_index)
+    tuple val(meta3), path(bqsr_table)
+    tuple val(meta4), path(intervals)
+    tuple val(meta5), path(fasta)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
@@ -25,6 +29,7 @@ process PARABRICKS_APPLYBQSR {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def interval_command = intervals ? intervals.collect{"--interval-file $it"}.join(' ') : ""
     def copy_index_command = bam_index ? "cp -L $bam_index `readlink -f $bam`.bai" : ""
+    def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
     """
     # parabricks complains when index is not a regular file in the same directory as the bam
     # copy the index to this path.
@@ -38,7 +43,7 @@ process PARABRICKS_APPLYBQSR {
         $interval_command \\
         --out-bam ${prefix}.bam \\
         --num-threads $task.cpus \\
-        --num-gpus $task.accelerator.request \\
+        $num_gpus \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/parabricks/applybqsr/meta.yml b/modules/nf-core/parabricks/applybqsr/meta.yml
index 09fdbacab1b..22f0c4c2067 100644
--- a/modules/nf-core/parabricks/applybqsr/meta.yml
+++ b/modules/nf-core/parabricks/applybqsr/meta.yml
@@ -23,18 +23,33 @@ input:
         type: file
         description: BAM file
         pattern: "*.bam"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information.
+          e.g. [ id:'test' ]
     - bam_index:
         type: file
         description: BAM index file
         pattern: "*.bai"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information.
+          e.g. [ id:'test' ]
     - bqsr_table:
         type: file
         description: Table from calculating BQSR. Output from parabricks/fq2bam or gatk4/baserecalibrator.
         pattern: "*.table"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sample information.
+          e.g. [ id:'test' ]
     - intervals:
         type: file
         description: intervals
-  - - meta2:
+  - - meta5:
         type: map
         description: |
           Groovy Map containing sample information
diff --git a/modules/nf-core/parabricks/applybqsr/tests/main.nf.test b/modules/nf-core/parabricks/applybqsr/tests/main.nf.test
new file mode 100644
index 00000000000..c85fd447b3d
--- /dev/null
+++ b/modules/nf-core/parabricks/applybqsr/tests/main.nf.test
@@ -0,0 +1,213 @@
+nextflow_process {
+
+    name "Test Process PARABRICKS_APPLYBQSR"
+    script "../main.nf"
+    process "PARABRICKS_APPLYBQSR"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "parabricks"
+    tag "parabricks/applybqsr"
+
+    test("sarscov2 - bam - pe") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = [
+                    [], []  // index not needed unless using intervals
+                ]
+                input[2] = [
+                    [ id:'bqsr_table'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true)
+                ]
+                input[3] = [
+                    [], []  // no intervals
+                ]
+                input[4] = [
+                    [ id:'reference'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    file(process.out.bai[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - pe - intervals") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test-index'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'bqsr_table'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ id:'intervals'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                ]
+                input[4] = [
+                    [ id:'reference'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                   ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    file(process.out.bai[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("human - cram - pe") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                ]
+                input[1] = [
+                    [], []  // index not needed unless using intervals
+                ]
+                input[2] = [
+                    [ id:'bqsr_table'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true)
+                ]
+                input[3] = [
+                    [], []  // no intervals
+                ]
+                input[4] = [
+                    [ id:'reference'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                   ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    file(process.out.bai[0][1]).name,
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+    test("human - cram - pe - intervals - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test-index'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'bqsr_table'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ id:'intervals'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
+                ]
+                input[4] = [
+                    [ id:'reference'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                   ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - bam - pe - intervals - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test-index'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'bqsr_table'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ id:'intervals'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                ]
+                input[4] = [
+                    [ id:'reference'],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                   ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap b/modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap
new file mode 100644
index 00000000000..c7a55002ac5
--- /dev/null
+++ b/modules/nf-core/parabricks/applybqsr/tests/main.nf.test.snap
@@ -0,0 +1,142 @@
+{
+    "human - cram - pe": {
+        "content": [
+            "2f11e4fe3390b8ad0a1852616fd1da04",
+            "test.bam.bai",
+            [
+                "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T08:40:58.540517299"
+    },
+    "sarscov2 - bam - pe": {
+        "content": [
+            "894549ee3ced6b5ca2eed2563a985217",
+            "test.bam.bai",
+            [
+                "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-30T10:55:02.759938278"
+    },
+    "sarscov2 - bam - pe - intervals": {
+        "content": [
+            "b194021b699cc5cf4b2b1f715e0b7b4c",
+            "test.bam.bai",
+            [
+                "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-30T11:20:43.476752722"
+    },
+    "sarscov2 - bam - pe - intervals - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-30T11:21:02.658767469"
+    },
+    "human - cram - pe - intervals - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,139b8f2a0926a26cf843ac23daace6d0"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-30T11:20:56.908929981"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/parabricks/fq2bam/main.nf b/modules/nf-core/parabricks/fq2bam/main.nf
index c1877bdf468..e6bf840c1f1 100644
--- a/modules/nf-core/parabricks/fq2bam/main.nf
+++ b/modules/nf-core/parabricks/fq2bam/main.nf
@@ -1,6 +1,7 @@
 process PARABRICKS_FQ2BAM {
     tag "$meta.id"
     label 'process_high'
+    label 'process_gpu'
 
     container "nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1"
 
diff --git a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap
index 50d96e78ffb..8d455f0efde 100644
--- a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap
+++ b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap
@@ -21,10 +21,10 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,c054e8254095319b660a92bdc07d990f"
+                    
                 ],
                 "3": [
-                    
+                    "versions.yml:md5,c054e8254095319b660a92bdc07d990f"
                 ],
                 "4": [
                     
@@ -65,10 +65,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-30T00:20:56.208782"
+        "timestamp": "2024-11-12T11:09:05.670189769"
     },
     "sarscov2 - fastq - pe - stub": {
         "content": [
@@ -92,10 +92,10 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,c054e8254095319b660a92bdc07d990f"
+                    
                 ],
                 "3": [
-                    
+                    "versions.yml:md5,c054e8254095319b660a92bdc07d990f"
                 ],
                 "4": [
                     
@@ -136,10 +136,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-30T00:35:07.267293"
+        "timestamp": "2024-11-12T11:09:56.252425453"
     },
     "sarscov2 - fastq - pe": {
         "content": [
diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap
index 265bb4bf917..cf06f28c7b3 100644
--- a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap
+++ b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap
@@ -21,15 +21,13 @@
                     ]
                 ],
                 "2": [
-                    [
-                        "alignment.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "3": [
                     
                 ],
                 "4": [
-                    "duplicate-metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    
                 ],
                 "5": [
                     "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf"
@@ -56,12 +54,10 @@
                     
                 ],
                 "duplicate_metrics": [
-                    "duplicate-metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    
                 ],
                 "qc_metrics": [
-                    [
-                        "alignment.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "versions": [
                     "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf"
@@ -69,10 +65,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-26T21:29:35.546741"
+        "timestamp": "2024-11-12T11:20:10.809580487"
     },
     "E. coli - fastq - pe - stub": {
         "content": [
@@ -96,15 +92,13 @@
                     ]
                 ],
                 "2": [
-                    [
-                        "alignment.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "3": [
                     
                 ],
                 "4": [
-                    "duplicate-metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    
                 ],
                 "5": [
                     "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf"
@@ -131,12 +125,10 @@
                     
                 ],
                 "duplicate_metrics": [
-                    "duplicate-metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    
                 ],
                 "qc_metrics": [
-                    [
-                        "alignment.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "versions": [
                     "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf"
@@ -144,10 +136,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.1",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-10-26T21:33:35.78287"
+        "timestamp": "2024-11-12T11:20:18.927598721"
     },
     "SRR389222 - fastq - se": {
         "content": [
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
index c86fb134d75..de10acc9fb2 100644
--- a/tests/config/nextflow.config
+++ b/tests/config/nextflow.config
@@ -25,6 +25,11 @@ if ("$PROFILE" == "singularity") {
     podman.enabled = true
     podman.userEmulation = true
     podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always"
+} else if ("$PROFILE" == "gpu") {
+    docker.runOptions       = '-u $(id -u):$(id -g) --gpus device=0'
+    apptainer.runOptions    = '--no-mount tmp --writable-tmpfs --nv'
+    singularity.runOptions  = '--no-mount tmp --writable-tmpfs --nv'
+    use_gpu                 = true
 } else {
     docker.enabled = true
     docker.userEmulation = false
diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
index 0bbe5e5b0c0..1bdf57d23c1 100644
--- a/tests/config/nf-test.config
+++ b/tests/config/nf-test.config
@@ -32,6 +32,12 @@ profiles {
         docker.enabled = true
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
+    gpu {
+        docker.runOptions       = '-u $(id -u):$(id -g) --gpus device=0'
+        apptainer.runOptions    = '--no-mount tmp --writable-tmpfs --nv'
+        singularity.runOptions  = '--no-mount tmp --writable-tmpfs --nv'
+        use_gpu                 = true
+    }
     docker_self_hosted {
         docker.enabled = true
         docker.fixOwnership = true
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 887e215cbe8..8a781b0c78c 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -449,9 +449,6 @@ ncbitools/vecscreen:
 oncocnv:
   - modules/nf-core/oncocnv/**
   - tests/modules/nf-core/oncocnv/**
-parabricks/applybqsr:
-  - modules/nf-core/parabricks/applybqsr/**
-  - tests/modules/nf-core/parabricks/applybqsr/**
 parabricks/dbsnp:
   - modules/nf-core/parabricks/dbsnp/**
   - tests/modules/nf-core/parabricks/dbsnp/**
diff --git a/tests/modules/nf-core/parabricks/applybqsr/main.nf b/tests/modules/nf-core/parabricks/applybqsr/main.nf
deleted file mode 100644
index 8da248632f8..00000000000
--- a/tests/modules/nf-core/parabricks/applybqsr/main.nf
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { PARABRICKS_APPLYBQSR } from '../../../../../modules/nf-core/parabricks/applybqsr/main.nf'
-
-workflow test_parabricks_applybqsr {
-    
-    input = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
-        [], // index not needed unless using intervals
-        file(params.test_data['sarscov2']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
-        []
-    ]
-    fasta = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-        ]
-
-    PARABRICKS_APPLYBQSR ( input, fasta )
-}
-
-workflow test_parabricks_applybqsr_intervals {
-    
-    input = [
-        [ id:'test'],
-        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']['illumina']['test_baserecalibrator_table'], checkIfExists: true),
-        file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
-    ]
-    fasta = [
-        [ id:'test'],
-        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-        ]
-        
-    PARABRICKS_APPLYBQSR ( input, fasta )
-}
diff --git a/tests/modules/nf-core/parabricks/applybqsr/nextflow.config b/tests/modules/nf-core/parabricks/applybqsr/nextflow.config
deleted file mode 100644
index 8730f1c4b93..00000000000
--- a/tests/modules/nf-core/parabricks/applybqsr/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/parabricks/applybqsr/test.yml b/tests/modules/nf-core/parabricks/applybqsr/test.yml
deleted file mode 100644
index 11c821cae01..00000000000
--- a/tests/modules/nf-core/parabricks/applybqsr/test.yml
+++ /dev/null
@@ -1,21 +0,0 @@
-- name: parabricks applybqsr test_parabricks_applybqsr
-  command: nextflow run ./tests/modules/nf-core/parabricks/applybqsr/ -entry test_parabricks_applybqsr -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/applybqsr/nextflow.config -stub-run
-  tags:
-    - parabricks/applybqsr
-    - parabricks
-  files:
-    - path: output/parabricks/test.bam
-      should_exist: true
-    - path: output/parabricks/test.bam.bai
-      should_exist: true
-
-- name: parabricks applybqsr test_parabricks_applybqsr_intervals
-  command: nextflow run ./tests/modules/nf-core/parabricks/applybqsr/ -entry test_parabricks_applybqsr_intervals -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/parabricks/applybqsr/nextflow.config -stub-run
-  tags:
-    - parabricks/applybqsr
-    - parabricks
-  files:
-    - path: output/parabricks/test.bam
-      should_exist: true
-    - path: output/parabricks/test.bam.bai
-      should_exist: true
diff --git a/tests/modules/nf-core/parabricks/applybqsr/test_GPU_config.txt b/tests/modules/nf-core/parabricks/applybqsr/test_GPU_config.txt
deleted file mode 100644
index 093a8b1afd1..00000000000
--- a/tests/modules/nf-core/parabricks/applybqsr/test_GPU_config.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    memory = "15 GB"
-    cpus  = 4
-    accelerator = 1
-}
-docker.runOptions = "--gpus all"
-singularity.runOptions = "--nv"
\ No newline at end of file

From 1c23afc032d7e340a7e4a17140b3847bf1cc0b18 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Fri, 15 Nov 2024 13:23:45 -0600
Subject: [PATCH 07/12] chore(deps): update dotnet monorepo to v9 (major)
 (#5846)

* chore(deps): update dotnet monorepo to v9

* build: Swap COPY for ADD

* build: Bump container version

---------

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Co-authored-by: Edmund Miller <git@edmundmiller.dev>
---
 modules/nf-core/wittyer/Dockerfile | 6 +++---
 modules/nf-core/wittyer/main.nf    | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/wittyer/Dockerfile b/modules/nf-core/wittyer/Dockerfile
index fbf732f32bd..5d1236d5985 100644
--- a/modules/nf-core/wittyer/Dockerfile
+++ b/modules/nf-core/wittyer/Dockerfile
@@ -1,12 +1,12 @@
-FROM mcr.microsoft.com/dotnet/sdk:6.0@sha256:6df1177e48b55272316d08f19cb383483af82aca5cdc67a76c414bc200847624 as builder
+FROM mcr.microsoft.com/dotnet/sdk:9.0@sha256:7d24e90a392e88eb56093e4eb325ff883ad609382a55d42f17fd557b997022ca as builder
 
+ADD https://github.com/Illumina/witty.er.git#v0.5.2 /src
 WORKDIR /src
-COPY . /src
 RUN cd Wittyer \
     && dotnet publish -f net6.0 -r linux-x64 -c Release -o /output \
     && chmod +x /output/Wittyer
 
-FROM mcr.microsoft.com/dotnet/runtime:6.0@sha256:437cda84bdce26ce074d88b63abeec567c7226d73e8b911605077468e1d5c8d5
+FROM mcr.microsoft.com/dotnet/runtime:9.0@sha256:1e5eb0ed94ca96a34a914456db80e48bd1bb7bc3e3c8eda5e2c3d89c153c3081
 
 LABEL git_repository=https://git.illumina.com/DASTE/Ilmn.Das.App.Wittyer.git
 WORKDIR /opt/Wittyer
diff --git a/modules/nf-core/wittyer/main.nf b/modules/nf-core/wittyer/main.nf
index 5cee35c8fd8..da0f7efbbd9 100644
--- a/modules/nf-core/wittyer/main.nf
+++ b/modules/nf-core/wittyer/main.nf
@@ -2,7 +2,7 @@ process WITTYER {
     tag "$meta.id"
     label 'process_single'
 
-    container "nf-core/wittyer:0.5.2.0"
+    container "nf-core/modules/wittyer:4c55c27c711b558f"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

From 21f230b8cca43755bf73470e6fd0290832a98aef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?=
 <mashehu@users.noreply.github.com>
Date: Sat, 16 Nov 2024 05:24:44 +0100
Subject: [PATCH 08/12] Add GPU-based tests (#6953)

* split nf-test section into its own action.yml and add gpu test cases

* add gpu profile

* Update test.yml

* add checkout action before running nf-test action

* add miniconda-setup step

* Update tests/config/nextflow.config

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

* try to fix composite action

* add profile info to include step, to avoid empty profile values

* touch fastqc to kick of some tests

* add gpu profile to nf-test.config

* fix miniconda setup step

* remove miniconda version pin

* try to exclude all non-gpu tests

* remove changed paths

* add check for changes in parabricks

* fix pip error

* add setup-python to main script

* remove conda defaults channels

---------

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
---
 .github/actions/nf-test-action/action.yml |  83 ++++++++
 .github/workflows/test.yml                | 234 +++-------------------
 .pre-commit-config.yaml                   |   2 +-
 modules/nf-core/fastqc/meta.yml           |   1 +
 tests/config/nextflow.config              |   5 -
 tests/config/nf-test.config               |   6 +
 6 files changed, 117 insertions(+), 214 deletions(-)
 create mode 100644 .github/actions/nf-test-action/action.yml

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
new file mode 100644
index 00000000000..4dd6df48919
--- /dev/null
+++ b/.github/actions/nf-test-action/action.yml
@@ -0,0 +1,83 @@
+name: "nf-test Action"
+description: "Runs nf-test with common setup steps"
+inputs:
+  path:
+    description: "Path to test"
+    required: true
+  profile:
+    description: "Profile to use"
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-java@v4
+      with:
+        distribution: "temurin"
+        java-version: "17"
+
+    - name: Setup Nextflow
+      uses: nf-core/setup-nextflow@v2
+
+    - name: Set up Python
+      uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      with:
+        python-version: "3.11"
+
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: "0.9.2"
+        install-pdiff: true
+
+    - name: Setup apptainer
+      if: contains(inputs.profile, 'singularity')
+      uses: eWaterCycle/setup-apptainer@main
+
+    - name: Set up Singularity
+      if: contains(inputs.profile, 'singularity')
+      shell: bash
+      run: |
+        mkdir -p $NXF_SINGULARITY_CACHEDIR
+        mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+    - name: Conda setup
+      if: ${{inputs.profile == 'conda'}}
+      uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
+      with:
+        auto-update-conda: true
+        conda-solver: libmamba
+        conda-remove-defaults: true
+
+    # Set up secrets
+    - name: Set up nextflow secrets
+      if: env.SENTIEON_ENCRYPTION_KEY != '' && env.SENTIEON_LICENSE_MESSAGE != ''
+      shell: bash
+      run: |
+        nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+
+    - name: Run nf-test
+      shell: bash
+      env:
+        SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
+        SENTIEON_AUTH_MECH: "GitHub Actions - token"
+      run: |
+        NFT_WORKDIR=~ \
+        nf-test test \
+          --profile=${{ inputs.profile }} \
+          --tap=test.tap \
+          --verbose \
+          ${{ inputs.path }}
+    - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
+      if: ${{ inputs.path != '' }}
+      with:
+        path: >-
+          test.tap
+
+    - name: Clean up
+      if: always()
+      shell: bash
+      run: |
+        sudo rm -rf /home/ubuntu/tests/
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4c22ed82bed..0ff73656067 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -35,6 +35,8 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
       - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+        with:
+          python-version: "3.11"
       - 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
@@ -86,8 +88,7 @@ jobs:
         with:
           fetch-depth: 2 # To retrieve the preceding commit.
 
-      # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented
-      - uses: mirpedrol/paths-filter@main
+      - uses: dorny/paths-filter@v3
         id: filter
         with:
           filters: "tests/config/pytest_modules.yml"
@@ -135,6 +136,7 @@ jobs:
 
       - name: debug
         run: |
+          echo ${{ steps.filter.outputs.components }}
           echo ${{ steps.outputs.outputs.modules }}
           echo ${{ steps.outputs.outputs.subworkflows }}
 
@@ -441,6 +443,7 @@ jobs:
           miniconda-version: "latest"
           channels: conda-forge,bioconda
           python-version: ${{ matrix.python-version }}
+          conda-remove-defaults: true
 
       - name: Conda setup
         run: |
@@ -485,7 +488,7 @@ jobs:
             !${{ github.workspace }}/.singularity
 
   nf-test:
-    runs-on: ${{ github.event.inputs.runners  || 'ubuntu-latest' }}
+    runs-on: ${{ github.event.inputs.runners || 'self-hosted' }}
     name: nf-test
     needs: [nf-test-changes]
     if: ( needs.nf-test-changes.outputs.paths != '[]' )
@@ -670,233 +673,47 @@ jobs:
 
     env:
       NXF_ANSI_LOG: false
-      NFTEST_VER: "0.9.0"
-      SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
-      SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
 
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
-        with:
-          distribution: "temurin"
-          java-version: "17"
-      - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v2
-
-      - name: Install nf-test
-        uses: nf-core/setup-nf-test@v1
-        with:
-          version: ${{ env.NFTEST_VER }}
-
-      - name: Setup apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Set up Python
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.11"
-
-      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
-        id: cache-pip-pdiff
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-pdiff
-          restore-keys: |
-            ${{ runner.os }}-pip-pdiff
-
-      - name: Install Python dependencies
-        run: python -m pip install --upgrade pip pdiff cryptography
-
-      - name: Set up miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@d2e6a045a86077fb6cad6f5adf368e9076ddaa8d # v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          channels: conda-forge,bioconda
-
-      - name: Conda setup
-        if: matrix.profile == 'conda'
-        run: |
-          conda clean -a
-          conda install -n base conda-libmamba-solver
-          conda config --set solver libmamba
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-
-      # Set up secrets
-      - name: Set up nextflow secrets
-        # TODO Only run if the tag includes `sentieon`
-        if: env.SENTIEON_ENCRYPTION_KEY != null && env.SENTIEON_LICENSE_MESSAGE != null
-        run: |
-          nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "${{ secrets.SENTIEON_LICENSE_MESSAGE }}")
-
-      # Test the module
-      - name: Run nf-test
-        if: ${{ matrix.path != '' }}
-        env:
-          NFT_DIFF: "pdiff"
-          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
-          SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
-          SENTIEON_AUTH_MECH: "GitHub Actions - token"
-        run: |
-          # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker
-          if [ "${{ matrix.profile }}" == "docker" ]; then
-            PROFILE="docker_self_hosted"
-          else
-            PROFILE=${{ matrix.profile }}
-          fi
-
-          NFT_WORKDIR=~ \
-          nf-test test \
-            --profile=${{ matrix.profile }} \
-            --tap=test.tap \
-            --verbose \
-            ${{ matrix.path }}
-
-      - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
-        if: ${{ matrix.path != '' }}
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - name: Run nf-test Action
+        uses: ./.github/actions/nf-test-action
         with:
-          path: >-
-            test.tap
-
-      - name: Clean up
-        if: always()
-        run: |
-          sudo rm -rf /home/ubuntu/tests/
+          path: ${{ matrix.path }}
+          profile: ${{ matrix.profile }}
 
   nf-test-gpu:
-    runs-on: ${{ github.event.inputs.runners  || 'gpu' }}
-    name: nf-test with GPUs
+    runs-on: "gpu"
+    name: nf-test-gpu
     needs: [nf-test-changes]
-    if: ( needs.nf-test-changes.outputs.paths != '[]' )
+    if: ( needs.nf-test-changes.outputs.paths != '[]' && contains(needs.nf-test-changes.outputs.paths, 'modules/nf-core/parabricks') )
     strategy:
       fail-fast: false
       matrix:
-        path: ["${{ fromJson(needs.nf-test-changes.outputs.paths) }}"]
-        profile: [conda, docker_self_hosted, singularity]
         include:
           - path: modules/nf-core/parabricks/applybqsr
+            profile: [docker_self_hosted, singularity]
           - path: modules/nf-core/parabricks/fq2bam
-          # - path: modules/nf-core/parabricks/fq2bammeth excluded - tackle in different PR
-        exclude:
-          - profile: conda
-            path: modules/nf-core/parabricks/fq2bam
-          - profile: conda
-            path: modules/nf-core/parabricks/fq2bammeth
-          - profile: conda
-            path: modules/nf-core/parabricks/applybqsr
+            profile: [docker_self_hosted, singularity]
+          - path: modules/nf-core/parabricks/fq2bammeth
+            profile: [docker_self_hosted, singularity]
     env:
       NXF_ANSI_LOG: false
-      NFTEST_VER: "0.9.0"
-      SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
-      SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
 
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
-
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
-        with:
-          distribution: "temurin"
-          java-version: "17"
-      - name: Setup Nextflow
-        uses: nf-core/setup-nextflow@v2
-
-      - name: Install nf-test
-        uses: nf-core/setup-nf-test@v1
-        with:
-          version: ${{ env.NFTEST_VER }}
-
-      - name: Setup apptainer
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-apptainer@main
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        run: |
-          mkdir -p $NXF_SINGULARITY_CACHEDIR
-          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
-
-      - name: Set up Python
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.11"
-
-      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # v4
-        id: cache-pip-pdiff
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-pdiff
-          restore-keys: |
-            ${{ runner.os }}-pip-pdiff
-
-      - name: Install Python dependencies
-        run: python -m pip install --upgrade pip pdiff cryptography
-
-      - name: Set up miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
-        with:
-          miniconda-version: "latest"
-          auto-update-conda: true
-          channels: conda-forge,bioconda
-
-      - name: Conda setup
-        if: matrix.profile == 'conda'
-        run: |
-          conda clean -a
-          conda install -n base conda-libmamba-solver
-          conda config --set solver libmamba
-          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
-          echo $(realpath python) >> $GITHUB_PATH
-
-      # Set up secrets
-      - name: Set up nextflow secrets
-        # TODO Only run if the tag includes `sentieon`
-        if: env.SENTIEON_ENCRYPTION_KEY != null && env.SENTIEON_LICENSE_MESSAGE != null
-        run: |
-          nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "${{ secrets.SENTIEON_LICENSE_MESSAGE }}")
-      # Test the module
-      - name: Run nf-test
-        if: ${{ matrix.path != '' }}
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
+      - name: Run nf-test Action
+        uses: ./.github/actions/nf-test-action
         env:
-          NFT_DIFF: "pdiff"
-          NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
+          SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }}
+          SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }}
           SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }}
           SENTIEON_AUTH_MECH: "GitHub Actions - token"
-        run: |
-          # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker
-          if [ "${{ matrix.profile }}" == "docker" ]; then
-            PROFILE="docker_self_hosted"
-          else
-            PROFILE=${{ matrix.profile }}
-          fi
-
-          NFT_WORKDIR=~ \
-          nf-test test \
-            --profile=${{ matrix.profile }},gpu \
-            --tap=test.tap \
-            --verbose \
-            ${{ matrix.path }}
-
-      - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1
-        if: ${{ matrix.path != '' }}
         with:
-          path: >-
-            test.tap
-
-      - name: Clean up
-        if: always()
-        run: |
-          sudo rm -rf /home/ubuntu/tests/
+          path: ${{ matrix.path }}
+          profile: ${{ matrix.profile }},gpu
 
   confirm-pass:
     runs-on: ubuntu-latest
@@ -910,6 +727,7 @@ jobs:
         pytest,
         nf-test-changes,
         nf-test,
+        nf-test-gpu,
       ]
     if: always()
     steps:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5d9bf144771..b97fd79f3a8 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.2.5
+          - prettier@3.3.3
   - repo: https://github.com/python-jsonschema/check-jsonschema
     rev: 0.29.4
     hooks:
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
index 4827da7af24..2b2e62b8aea 100644
--- a/modules/nf-core/fastqc/meta.yml
+++ b/modules/nf-core/fastqc/meta.yml
@@ -11,6 +11,7 @@ tools:
         FastQC gives general quality metrics about your reads.
         It provides information about the quality score distribution
         across your reads, the per base sequence content (%A/C/G/T).
+
         You get information about adapter contamination and other
         overrepresented sequences.
       homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
index de10acc9fb2..c86fb134d75 100644
--- a/tests/config/nextflow.config
+++ b/tests/config/nextflow.config
@@ -25,11 +25,6 @@ if ("$PROFILE" == "singularity") {
     podman.enabled = true
     podman.userEmulation = true
     podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always"
-} else if ("$PROFILE" == "gpu") {
-    docker.runOptions       = '-u $(id -u):$(id -g) --gpus device=0'
-    apptainer.runOptions    = '--no-mount tmp --writable-tmpfs --nv'
-    singularity.runOptions  = '--no-mount tmp --writable-tmpfs --nv'
-    use_gpu                 = true
 } else {
     docker.enabled = true
     docker.userEmulation = false
diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
index 1bdf57d23c1..f651ff4d89d 100644
--- a/tests/config/nf-test.config
+++ b/tests/config/nf-test.config
@@ -43,6 +43,12 @@ profiles {
         docker.fixOwnership = true
         docker.runOptions = '--platform=linux/amd64'
     }
+    gpu {
+        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
+        apptainer.runOptions    = '--nv'
+        singularity.runOptions  = '--nv'
+        use_gpu                 = true
+    }
 }
 
 docker.registry = 'quay.io'

From 484afd16770cf3c466a6c385e33746c877656663 Mon Sep 17 00:00:00 2001
From: Daniel Schmitz <daniel.schmitz@gu.se>
Date: Sat, 16 Nov 2024 06:22:19 +0100
Subject: [PATCH 09/12] Added module trgt/genotype (#7002)

* Imported genotype module from trgt branch

* Fixed test issues

---------

Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
---
 modules/nf-core/trgt/genotype/environment.yml |   7 +
 modules/nf-core/trgt/genotype/main.nf         |  56 +++++
 modules/nf-core/trgt/genotype/meta.yml        |  98 +++++++++
 .../nf-core/trgt/genotype/tests/main.nf.test  | 154 ++++++++++++++
 .../trgt/genotype/tests/main.nf.test.snap     | 198 ++++++++++++++++++
 5 files changed, 513 insertions(+)
 create mode 100644 modules/nf-core/trgt/genotype/environment.yml
 create mode 100644 modules/nf-core/trgt/genotype/main.nf
 create mode 100644 modules/nf-core/trgt/genotype/meta.yml
 create mode 100644 modules/nf-core/trgt/genotype/tests/main.nf.test
 create mode 100644 modules/nf-core/trgt/genotype/tests/main.nf.test.snap

diff --git a/modules/nf-core/trgt/genotype/environment.yml b/modules/nf-core/trgt/genotype/environment.yml
new file mode 100644
index 00000000000..721e0df3d5f
--- /dev/null
+++ b/modules/nf-core/trgt/genotype/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::trgt=1.2.0"
diff --git a/modules/nf-core/trgt/genotype/main.nf b/modules/nf-core/trgt/genotype/main.nf
new file mode 100644
index 00000000000..3fa0b7b4e59
--- /dev/null
+++ b/modules/nf-core/trgt/genotype/main.nf
@@ -0,0 +1,56 @@
+process TRGT_GENOTYPE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/trgt:1.2.0--h9ee0642_0':
+        'biocontainers/trgt:1.2.0--h9ee0642_0' }"
+
+    input:
+    tuple val(meta) , path(bam), path(bai), val(karyotype)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(repeats)
+
+    output:
+    tuple val(meta), path("*.vcf.gz")      , emit: vcf
+    tuple val(meta), path("*.spanning.bam"), emit: bam     , optional: true
+    path "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def karyo = karyotype ? "--karyotype ${karyotype}" : ""
+    """
+    trgt genotype \\
+        $args \\
+        --genome ${fasta} \\
+        --reads ${bam} \\
+        --repeats ${repeats} \\
+        ${karyo} \\
+        --threads ${task.cpus} \\
+        --output-prefix ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        trgt: \$(trgt --version |& sed '1!d ; s/trgt //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.spanning.bam
+    echo "" | gzip > ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        trgt: \$(trgt --version |& sed '1!d ; s/trgt //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/trgt/genotype/meta.yml b/modules/nf-core/trgt/genotype/meta.yml
new file mode 100644
index 00000000000..bd17e4cae82
--- /dev/null
+++ b/modules/nf-core/trgt/genotype/meta.yml
@@ -0,0 +1,98 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "trgt_genotype"
+description: Tandem repeat genotyping from PacBio HiFi data
+keywords:
+  - repeat expansion
+  - pacbio
+  - genomics
+tools:
+  - "trgt":
+      description: "Tandem repeat genotyping and visualization from PacBio HiFi data"
+      homepage: "https://github.com/PacificBiosciences/trgt"
+      documentation: "https://github.com/PacificBiosciences/trgt/blob/main/docs/tutorial.md"
+      tool_dev_url: "https://github.com/PacificBiosciences/trgt"
+      doi: "10.1038/s41587-023-02057-3"
+      licence:
+        ["Pacific Biosciences Software License (https://github.com/PacificBiosciences/trgt/blob/main/LICENSE.md)"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - bam:
+        type: file
+        description: Sorted BAM file
+        pattern: "*.bam"
+    - bai:
+        type: file
+        description: "Index of the BAM file"
+        pattern: "*.bam"
+    - karyotype:
+        type: string
+        description: "Karyotype of the sample. Either XX or XY. Defaults to XX if not given"
+        enum:
+          - XX
+          - XY
+  - - meta2:
+        type: map
+        description: |
+          Groovy map containing reference information
+          e.g. `[ id: 'genome' ]`
+    - fasta:
+        type: file
+        description: "FASTA reference file"
+        pattern: "*.{fasta,fa,fna}"
+  - - meta3:
+        type: map
+        description: |
+          Groovy map containing reference information
+          e.g. `[ id: 'genome' ]`
+    - fai:
+        type: file
+        description: "Index for FASTA file"
+        pattern: "*.fai"
+  - - meta4:
+        type: map
+        description: |
+          Groovy map containing repeat information
+          e.g. `[ id: 'repeats' ]`
+    - repeats:
+        type: file
+        description: "BED file with repeat coordinates"
+        pattern: "*.bed"
+
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.vcf.gz":
+          type: file
+          description: "VCF file with repeat genotypes"
+          pattern: "*.vcf.gz"
+  - bam:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.spanning.bam":
+          type: file
+          description: BAM file with pieces of reads aligning to repeats
+          pattern: "*.spanning.bam"
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@Schmytzi"
+  - "@fellen31"
+maintainers:
+  - "@Schmytzi"
diff --git a/modules/nf-core/trgt/genotype/tests/main.nf.test b/modules/nf-core/trgt/genotype/tests/main.nf.test
new file mode 100644
index 00000000000..d93a2e9603c
--- /dev/null
+++ b/modules/nf-core/trgt/genotype/tests/main.nf.test
@@ -0,0 +1,154 @@
+// nf-core modules test trgt
+nextflow_process {
+
+    name "Test Process TRGT_GENOTYPE"
+    script "../main.nf"
+    process "TRGT_GENOTYPE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "trgt"
+    tag "trgt/genotype"
+    tag "samtools/faidx"
+    tag "gunzip"
+
+    setup {
+        run("GUNZIP"){
+            script "../../../gunzip/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id : 'chr22' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22_chr22_KI270734v1_random/sequence/genome.fa.gz', checkIfExists: true)
+                ]
+            """
+            }
+        }
+        run("SAMTOOLS_FAIDX"){
+            script "../../../samtools/faidx/main.nf"
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip
+                input[1] = [[],[]]
+                """
+            }
+        }
+    }
+
+    test("homo sapiens - [bam,bai,XX], [fa,fai], bed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                    'XX'
+                ]
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                            .collectFile(name : 'repeats.bed', newLine: false)
+                            .map { file -> [ [ id : 'chr22' ], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - [bam,bai,[]], [fa,fai], bed") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                    []
+                ]
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                            .collectFile(name : 'repeats.bed', newLine: false)
+                            .map { file -> [ [ id : 'chr22' ], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - [bam,bai,XX], [fa,fai], bed - stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                    'XX'
+                ]
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                                .collectFile(name : 'repeats.bed', newLine: false)
+                                .map { file -> [ [ id : 'chr22' ], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - [bam,bai,[]], [fa,fai], bed - stub") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                    []
+                ]
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                            .collectFile(name : 'repeats.bed', newLine: false)
+                            .map { file -> [ [ id : 'chr22' ], file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/trgt/genotype/tests/main.nf.test.snap b/modules/nf-core/trgt/genotype/tests/main.nf.test.snap
new file mode 100644
index 00000000000..9e50fb81eb3
--- /dev/null
+++ b/modules/nf-core/trgt/genotype/tests/main.nf.test.snap
@@ -0,0 +1,198 @@
+{
+    "homo sapiens - [bam,bai,XX], [fa,fai], bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,4e5b6028e3ea3d06829ca18af1cc492e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,645a2c199d04aaf733ce84247f0b0f37"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,645a2c199d04aaf733ce84247f0b0f37"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,4e5b6028e3ea3d06829ca18af1cc492e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-15T16:07:55.029938504"
+    },
+    "homo sapiens - [bam,bai,[]], [fa,fai], bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-15T16:08:33.937952067"
+    },
+    "homo sapiens - [bam,bai,XX], [fa,fai], bed - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-15T16:16:39.197756426"
+    },
+    "homo sapiens - [bam,bai,[]], [fa,fai], bed": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.spanning.bam:md5,8d6d1bf813109870692d2f20d59399e7"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,0337e3287dcc71728c36c185dae7738f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b773615cf974b094032306822d32017b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-15T16:08:07.631383773"
+    }
+}
\ No newline at end of file

From 48f98fa1f47094df9e0847a0d0f45d8448eaee1e Mon Sep 17 00:00:00 2001
From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Date: Sat, 16 Nov 2024 11:12:05 +0530
Subject: [PATCH 10/12] Fastq align dedup bismark (#6998)

* init subworkflow

* bismark + bismark_hisat tests

* update coverage2cytosine outputs

* update meta, tests

* rm index from snapshot

* Apply suggestions from code review

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

* apply suggestions from code review and improve tests

* rm extra params from test config

---------

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
---
 .../nf-core/fastq_align_dedup_bismark/main.nf | 153 +++++
 .../fastq_align_dedup_bismark/meta.yml        | 136 ++++
 .../tests/main.nf.test                        | 336 ++++++++++
 .../tests/main.nf.test.snap                   | 612 ++++++++++++++++++
 .../tests/nextflow.config                     |  15 +
 5 files changed, 1252 insertions(+)
 create mode 100644 subworkflows/nf-core/fastq_align_dedup_bismark/main.nf
 create mode 100644 subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml
 create mode 100644 subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test
 create mode 100644 subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap
 create mode 100644 subworkflows/nf-core/fastq_align_dedup_bismark/tests/nextflow.config

diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf b/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf
new file mode 100644
index 00000000000..1497e5adda8
--- /dev/null
+++ b/subworkflows/nf-core/fastq_align_dedup_bismark/main.nf
@@ -0,0 +1,153 @@
+include { BISMARK_ALIGN                                 } from '../../../modules/nf-core/bismark/align/main'
+include { BISMARK_DEDUPLICATE                           } from '../../../modules/nf-core/bismark/deduplicate/main'
+include { BISMARK_METHYLATIONEXTRACTOR                  } from '../../../modules/nf-core/bismark/methylationextractor/main'
+include { BISMARK_COVERAGE2CYTOSINE                     } from '../../../modules/nf-core/bismark/coverage2cytosine/main'
+include { BISMARK_REPORT                                } from '../../../modules/nf-core/bismark/report/main'
+include { BISMARK_SUMMARY                               } from '../../../modules/nf-core/bismark/summary/main'
+include { SAMTOOLS_SORT as SAMTOOLS_SORT_DEDUPLICATED   } from '../../../modules/nf-core/samtools/sort/main'
+include { SAMTOOLS_INDEX as SAMTOOLS_INDEX_DEDUPLICATED } from '../../../modules/nf-core/samtools/index/main'
+
+workflow FASTQ_ALIGN_DEDUP_BISMARK {
+
+    take:
+    ch_reads             // channel: [ val(meta), [ reads ] ]
+    ch_fasta             // channel: [ val(meta), [ fasta ] ]
+    ch_bismark_index     // channel: [ val(meta), [ bismark index ] ]
+    skip_deduplication   // boolean: whether to deduplicate alignments
+    cytosine_report      // boolean: whether the run coverage2cytosine
+
+    main:
+    ch_versions                   = Channel.empty()
+    ch_coverage2cytosine_coverage = Channel.empty()
+    ch_coverage2cytosine_report   = Channel.empty()
+    ch_coverage2cytosine_summary  = Channel.empty()
+    ch_methylation_bedgraph       = Channel.empty()
+    ch_methylation_calls          = Channel.empty()
+    ch_methylation_coverage       = Channel.empty()
+    ch_methylation_report         = Channel.empty()
+    ch_methylation_mbias          = Channel.empty()
+    ch_bismark_report             = Channel.empty()
+    ch_bismark_summary            = Channel.empty()
+    ch_multiqc_files              = Channel.empty()
+
+    /*
+     * Align with bismark
+     */
+    BISMARK_ALIGN (
+        ch_reads,
+        ch_fasta,
+        ch_bismark_index
+    )
+    ch_versions = ch_versions.mix(BISMARK_ALIGN.out.versions)
+
+    if (skip_deduplication) {
+        alignments        = BISMARK_ALIGN.out.bam
+        alignment_reports = BISMARK_ALIGN.out.report.map{ meta, report -> [ meta, report, [] ] }
+    } else {
+        /*
+        * Run deduplicate_bismark
+        */
+        BISMARK_DEDUPLICATE (
+            BISMARK_ALIGN.out.bam
+        )
+        alignments        = BISMARK_DEDUPLICATE.out.bam
+        alignment_reports = BISMARK_ALIGN.out.report.join(BISMARK_DEDUPLICATE.out.report)
+        ch_versions       = ch_versions.mix(BISMARK_DEDUPLICATE.out.versions)
+    }
+
+    /*
+     * Run bismark_methylation_extractor
+     */
+    BISMARK_METHYLATIONEXTRACTOR (
+        alignments,
+        ch_bismark_index
+    )
+    ch_methylation_bedgraph = BISMARK_METHYLATIONEXTRACTOR.out.bedgraph
+    ch_methylation_calls    = BISMARK_METHYLATIONEXTRACTOR.out.methylation_calls
+    ch_methylation_coverage = BISMARK_METHYLATIONEXTRACTOR.out.coverage
+    ch_methylation_report   = BISMARK_METHYLATIONEXTRACTOR.out.report
+    ch_methylation_mbias    = BISMARK_METHYLATIONEXTRACTOR.out.mbias
+    ch_versions             = ch_versions.mix(BISMARK_METHYLATIONEXTRACTOR.out.versions)
+
+    /*
+     * Run bismark coverage2cytosine
+     */
+    if (cytosine_report) {
+        BISMARK_COVERAGE2CYTOSINE (
+            BISMARK_METHYLATIONEXTRACTOR.out.coverage,
+            ch_fasta,
+            ch_bismark_index
+        )
+        ch_coverage2cytosine_coverage = BISMARK_COVERAGE2CYTOSINE.out.coverage
+        ch_coverage2cytosine_report   = BISMARK_COVERAGE2CYTOSINE.out.report
+        ch_coverage2cytosine_summary  = BISMARK_COVERAGE2CYTOSINE.out.summary
+        ch_versions                   = ch_versions.mix(BISMARK_COVERAGE2CYTOSINE.out.versions)
+    }
+
+    /*
+     * Generate bismark sample reports
+     */
+    BISMARK_REPORT (
+        alignment_reports
+            .join(ch_methylation_report)
+            .join(ch_methylation_mbias)
+    )
+    ch_bismark_report = BISMARK_REPORT.out.report
+    ch_versions       = ch_versions.mix(BISMARK_REPORT.out.versions)
+
+    /*
+     * Generate bismark summary report
+     */
+    BISMARK_SUMMARY (
+        BISMARK_ALIGN.out.bam.collect{ meta, bam -> bam.name },
+        alignment_reports.collect{ meta, align_report, dedup_report -> align_report },
+        alignment_reports.collect{ meta, align_report, dedup_report -> dedup_report }.ifEmpty([]),
+        BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ meta, report -> report },
+        BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ meta, mbias -> mbias }
+    )
+    ch_bismark_summary = BISMARK_SUMMARY.out.summary
+    ch_versions        = ch_versions.mix(BISMARK_SUMMARY.out.versions)
+
+    /*
+     * MODULE: Run samtools sort on dedup bam
+     */
+    SAMTOOLS_SORT_DEDUPLICATED (
+        alignments,
+        [[:],[]] // [ [meta], [fasta]]
+    )
+    ch_versions = ch_versions.mix(SAMTOOLS_SORT_DEDUPLICATED.out.versions)
+
+    /*
+     * MODULE: Run samtools index on dedup bam
+     */
+    SAMTOOLS_INDEX_DEDUPLICATED (
+        SAMTOOLS_SORT_DEDUPLICATED.out.bam
+    )
+    ch_versions = ch_versions.mix(SAMTOOLS_INDEX_DEDUPLICATED.out.versions)
+
+    /*
+     * Collect MultiQC inputs
+     */
+    ch_multiqc_files = BISMARK_SUMMARY.out.summary
+                        .mix(alignment_reports.collect{ meta, align_report, dedup_report -> align_report })
+                        .mix(alignment_reports.collect{ meta, align_report, dedup_report -> dedup_report })
+                        .mix(BISMARK_METHYLATIONEXTRACTOR.out.report.collect{ meta, report -> report })
+                        .mix(BISMARK_METHYLATIONEXTRACTOR.out.mbias.collect{ meta, mbias -> mbias })
+                        .mix(BISMARK_REPORT.out.report.collect{ meta, report -> report })
+
+    emit:
+    dedup_bam                  = SAMTOOLS_SORT_DEDUPLICATED.out.bam  // channel: [ val(meta), [ bam ] ]
+    dedup_bam_index            = SAMTOOLS_INDEX_DEDUPLICATED.out.bai // channel: [ val(meta), [ bai ] ]
+    coverage2cytosine_coverage = ch_coverage2cytosine_coverage       // channel: [ val(meta), [ coverage ] ]
+    coverage2cytosine_report   = ch_coverage2cytosine_report         // channel: [ val(meta), [ report ] ]
+    coverage2cytosine_summary  = ch_coverage2cytosine_summary        // channel: [ val(meta), [ summary ] ]
+    methylation_bedgraph       = ch_methylation_bedgraph             // channel: [ val(meta), [ bedgraph ] ]
+    methylation_calls          = ch_methylation_calls                // channel: [ val(meta), [ methylation_calls ] ]
+    methylation_coverage       = ch_methylation_coverage             // channel: [ val(meta), [ coverage ] ]
+    methylation_report         = ch_methylation_report               // channel: [ val(meta), [ report ] ]
+    methylation_mbias          = ch_methylation_mbias                // channel: [ val(meta), [ mbias ] ]
+    bismark_report             = ch_bismark_report                   // channel: [ val(meta), [ report ] ]
+    bismark_summary            = ch_bismark_summary                  // channel: [ val(meta), [ summary ] ]
+    multiqc                    = ch_multiqc_files                    // path: *{html,txt}
+    versions                   = ch_versions                         // path: *.version.txt
+}
diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml b/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml
new file mode 100644
index 00000000000..4f3aa80b946
--- /dev/null
+++ b/subworkflows/nf-core/fastq_align_dedup_bismark/meta.yml
@@ -0,0 +1,136 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "fastq_align_dedup_bismark"
+description: Align BS-Seq reads to a reference genome using bismark, deduplicate and sort
+keywords:
+  - bismark
+  - 3-letter genome
+  - map
+  - methylation
+  - 5mC
+  - methylseq
+  - bisulphite
+  - bisulfite
+  - bam
+components:
+  - bismark/align
+  - samtools/sort
+  - samtools/index
+  - bismark/deduplicate
+  - bismark/methylationextractor
+  - bismark/coverage2cytosine
+  - bismark/report
+  - bismark/summary
+input:
+  - ch_reads:
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+        Structure: [ val(meta), [ path(reads) ] ]
+      pattern: "*.{fastq,fastq.gz}"
+  - ch_fasta:
+      type: file
+      description: |
+        Structure: [ val(meta), path(fasta) ]
+      pattern: "*.{fa,fa.gz}"
+  - ch_index:
+      description: |
+        Bismark genome index files
+        Structure: [ val(meta), path(index) ]
+      pattern: "BismarkIndex"
+  - skip_deduplication:
+      type: boolean
+      description: |
+        Skip deduplication of aligned reads
+  - cytosine_report:
+      type: boolean
+      description: |
+        Produce coverage2cytosine reports that relates methylation calls back to genomic cytosine contexts
+output:
+  - dedup_bam:
+      type: file
+      description: |
+        Channel containing deduplicated BAM files.
+        Structure: [ val(meta), path(bam) ]
+      pattern: "*.bam"
+  - dedup_bam_index:
+      type: file
+      description: |
+        Channel containing deduplicated BAM index files.
+        Structure: [ val(meta), path(bam.bai) ]
+      pattern: "*.bai"
+  - coverage2cytosine_coverage:
+      type: file
+      description: |
+        Channel containing coverage information from coverage2cytosine.
+        Structure: [ val(meta), path(coverage.txt) ]
+      pattern: "*.cov.gz"
+  - coverage2cytosine_report:
+      type: file
+      description: |
+        Channel containing report from coverage2cytosine summarizing cytosine methylation coverage.
+        Structure: [ val(meta), path(report.txt) ]
+      pattern: "*report.txt.gz"
+  - coverage2cytosine_summary:
+      type: file
+      description: |
+        Channel containing summary information from coverage2cytosine.
+        Structure: [ val(meta), path(summary.txt) ]
+      pattern: "*cytosine_context_summary.txt"
+  - methylation_bedgraph:
+      type: file
+      description: |
+        Channel containing methylation data in bedGraph format.
+        Structure: [ val(meta), path(methylation.bedgraph) ]
+      pattern: "*.bedGraph.gz"
+  - methylation_calls:
+      type: file
+      description: |
+        Channel containing methylation call data.
+        Structure: [ val(meta), path(calls.txt) ]
+      pattern: "*.txt.gz"
+  - methylation_coverage:
+      type: file
+      description: |
+        Channel containing methylation coverage data.
+        Structure: [ val(meta), path(coverage.txt) ]
+      pattern: "*.cov.gz"
+  - methylation_report:
+      type: file
+      description: |
+        Channel containing methylation report detailing methylation patterns.
+        Structure: [ val(meta), path(report.txt) ]
+      pattern: "*_splitting_report.txt"
+  - methylation_mbias:
+      type: file
+      description: |
+        Channel containing M-bias report showing methylation bias across read positions.
+        Structure: [ val(meta), path(mbias.txt) ]
+      pattern: "*.M-bias.txt"
+  - bismark_report:
+      type: file
+      description: |
+        Channel containing Bismark report with mapping and methylation statistics.
+        Structure: [ val(meta), path(bismark_report.txt) ]
+      pattern: "*report.{html,txt}"
+  - bismark_summary:
+      type: file
+      description: |
+        Channel containing Bismark summary report.
+        Structure: [ val(meta), path(bismark_summary.txt) ]
+      pattern: "*report.{html,txt}"
+  - multiqc:
+      type: file
+      description: |
+        Channel containing MultiQC report aggregating results across samples.
+        Structure: [ val(meta), path(multiqc_report.html) ]
+      pattern: "*.html"
+  - versions:
+      type: file
+      description: |
+        File containing software versions.
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+authors:
+  - "@sateeshperi"
+maintainers:
+  - "@sateeshperi"
diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test
new file mode 100644
index 00000000000..f30c4344449
--- /dev/null
+++ b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test
@@ -0,0 +1,336 @@
+nextflow_workflow {
+
+    name "Test Subworkflow FASTQ_ALIGN_DEDUP_BISMARK"
+    script "../main.nf"
+    workflow "FASTQ_ALIGN_DEDUP_BISMARK"
+    config "./nextflow.config"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/fastq_align_dedup_bismark"
+    tag "bismark/align"
+    tag "samtools/sort"
+    tag "samtools/index"
+    tag "bismark/deduplicate"
+    tag "bismark/methylationextractor"
+    tag "bismark/coverage2cytosine"
+    tag "bismark/report"
+    tag "bismark/summary"
+    tag "untar"
+
+    setup {
+        run("UNTAR", alias: "BOWTIE2") {
+            script "../../../../modules/nf-core/untar/main.nf"
+            process {
+                """
+                input[0] = [
+                    [:],
+                    file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Bowtie2_Index.tar.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        run("UNTAR", alias: "HISAT2") {
+            script "../../../../modules/nf-core/untar/main.nf"
+            process {
+                """
+                input[0] = [
+                    [:],
+                    file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/Hisat2_Index.tar.gz', checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("Params: bismark | default") {
+
+        when {
+            params {
+                aligner            = "bismark"
+                cytosine_report    = false
+                skip_deduplication = false
+            }
+
+            workflow {
+                """
+                input[0] = Channel.of([
+                            [ id:'test', single_end:true ],
+                            file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                            [:],
+                            file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                ])
+                input[2] = BOWTIE2.out.untar
+                input[3] = params.skip_deduplication
+                input[4] = params.cytosine_report
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.dedup.collect { bam(it[1]).getReadsMD5() },
+                    workflow.out.dedup_bam_index.collect { meta, bai -> file(bai).name },
+                    workflow.out.coverage2cytosine_coverage,
+                    workflow.out.coverage2cytosine_report,
+                    workflow.out.coverage2cytosine_summary,
+                    workflow.out.methylation_bedgraph,
+                    workflow.out.methylation_calls,
+                    workflow.out.methylation_coverage,
+                    workflow.out.methylation_report,
+                    workflow.out.methylation_mbias,
+                    workflow.out.bismark_report.collect { meta, report -> file(report).name },
+                    workflow.out.bismark_summary[0][1],
+                    workflow.out.multiqc.flatten().collect { path -> file(path).name },
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("Params: bismark | skip_deduplication") {
+
+        when {
+            params {
+                aligner            = "bismark"
+                skip_deduplication = true
+            }
+
+            workflow {
+                """
+                input[0] = Channel.of([
+                            [ id:'test', single_end:true ],
+                            file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                            [:],
+                            file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                ])
+                input[2] = BOWTIE2.out.untar
+                input[3] = params.skip_deduplication
+                input[4] = params.cytosine_report
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.dedup.collect { bam(it[1]).getReadsMD5() },
+                    workflow.out.dedup_bam_index.collect { meta, bai -> file(bai).name },
+                    workflow.out.coverage2cytosine_coverage,
+                    workflow.out.coverage2cytosine_report,
+                    workflow.out.coverage2cytosine_summary,
+                    workflow.out.methylation_bedgraph,
+                    workflow.out.methylation_calls,
+                    workflow.out.methylation_coverage,
+                    workflow.out.methylation_report,
+                    workflow.out.methylation_mbias,
+                    workflow.out.bismark_report.collect { meta, report -> file(report).name },
+                    workflow.out.bismark_summary[0][1],
+                    workflow.out.multiqc.flatten().collect { path -> file(path).name },
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("Params: bismark | cytosine_report") {
+
+        when {
+            params {
+                aligner         = "bismark"
+                cytosine_report = true
+            }
+
+            workflow {
+                """
+                input[0] = Channel.of([
+                            [ id:'test', single_end:true ],
+                            file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                            [:],
+                            file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                ])
+                input[2] = BOWTIE2.out.untar
+                input[3] = params.skip_deduplication
+                input[4] = params.cytosine_report
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.dedup.collect { bam(it[1]).getReadsMD5() },
+                    workflow.out.dedup_bam_index.collect { meta, bai -> file(bai).name },
+                    workflow.out.coverage2cytosine_coverage,
+                    workflow.out.coverage2cytosine_report,
+                    workflow.out.coverage2cytosine_summary,
+                    workflow.out.methylation_bedgraph,
+                    workflow.out.methylation_calls,
+                    workflow.out.methylation_coverage,
+                    workflow.out.methylation_report,
+                    workflow.out.methylation_mbias,
+                    workflow.out.bismark_report.collect { meta, report -> file(report).name },
+                    workflow.out.bismark_summary[0][1],
+                    workflow.out.multiqc.flatten().collect { path -> file(path).name },
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("Params: bismark_hisat | default") {
+
+        when {
+            params {
+                aligner            = "bismark_hisat"
+                cytosine_report    = false
+                skip_deduplication = false
+            }
+
+            workflow {
+                """
+                input[0] = Channel.of([
+                            [ id:'test', single_end:true ],
+                            file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                            [:],
+                            file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                ])
+                input[2] = HISAT2.out.untar
+                input[3] = params.skip_deduplication
+                input[4] = params.cytosine_report
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.dedup.collect { bam(it[1]).getReadsMD5() },
+                    workflow.out.dedup_bam_index.collect { meta, bai -> file(bai).name },
+                    workflow.out.coverage2cytosine_coverage,
+                    workflow.out.coverage2cytosine_report,
+                    workflow.out.coverage2cytosine_summary,
+                    workflow.out.methylation_bedgraph,
+                    workflow.out.methylation_calls,
+                    workflow.out.methylation_coverage,
+                    workflow.out.methylation_report,
+                    workflow.out.methylation_mbias,
+                    workflow.out.bismark_report.collect { meta, report -> file(report).name },
+                    workflow.out.bismark_summary[0][1],
+                    workflow.out.multiqc.flatten().collect { path -> file(path).name },
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("Params: bismark_hisat | skip_deduplication") {
+
+        when {
+            params {
+                aligner            = "bismark_hisat"
+                skip_deduplication = true
+            }
+
+            workflow {
+                """
+                input[0] = Channel.of([
+                            [ id:'test', single_end:true ],
+                            file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                            [:],
+                            file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                ])
+                input[2] = HISAT2.out.untar
+                input[3] = params.skip_deduplication
+                input[4] = params.cytosine_report
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.dedup.collect { bam(it[1]).getReadsMD5() },
+                    workflow.out.dedup_bam_index.collect { meta, bai -> file(bai).name },
+                    workflow.out.coverage2cytosine_coverage,
+                    workflow.out.coverage2cytosine_report,
+                    workflow.out.coverage2cytosine_summary,
+                    workflow.out.methylation_bedgraph,
+                    workflow.out.methylation_calls,
+                    workflow.out.methylation_coverage,
+                    workflow.out.methylation_report,
+                    workflow.out.methylation_mbias,
+                    workflow.out.bismark_report.collect { meta, report -> file(report).name },
+                    workflow.out.bismark_summary[0][1],
+                    workflow.out.multiqc.flatten().collect { path -> file(path).name },
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+
+    test("Params: bismark_hisat | cytosine_report") {
+
+        when {
+            params {
+                aligner            = "bismark_hisat"
+                cytosine_report    = true
+            }
+
+            workflow {
+                """
+                input[0] = Channel.of([
+                            [ id:'test', single_end:true ],
+                            file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                            [:],
+                            file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true)
+                ])
+                input[2] = HISAT2.out.untar
+                input[3] = params.skip_deduplication
+                input[4] = params.cytosine_report
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.dedup.collect { bam(it[1]).getReadsMD5() },
+                    workflow.out.dedup_bam_index.collect { meta, bai -> file(bai).name },
+                    workflow.out.coverage2cytosine_coverage,
+                    workflow.out.coverage2cytosine_report,
+                    workflow.out.coverage2cytosine_summary,
+                    workflow.out.methylation_bedgraph,
+                    workflow.out.methylation_calls,
+                    workflow.out.methylation_coverage,
+                    workflow.out.methylation_report,
+                    workflow.out.methylation_mbias,
+                    workflow.out.bismark_report.collect { meta, report -> file(report).name },
+                    workflow.out.bismark_summary[0][1],
+                    workflow.out.multiqc.flatten().collect { path -> file(path).name },
+                    workflow.out.versions
+                    ).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap
new file mode 100644
index 00000000000..b8f199fb126
--- /dev/null
+++ b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/main.nf.test.snap
@@ -0,0 +1,612 @@
+{
+    "Params: bismark | skip_deduplication": {
+        "content": [
+            [
+                
+            ],
+            [
+                "test.sorted.bam.bai"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_bt2.bedGraph.gz:md5,6896f135c70e2f4944cb43260a687c6c"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    [
+                        "CHG_OB_SRR389222_sub1_bismark_bt2.txt.gz:md5,11ae58ebe6513375468ebe63a521d6e3",
+                        "CHG_OT_SRR389222_sub1_bismark_bt2.txt.gz:md5,d0754aef3f7066881bdee1adf72b4bd1",
+                        "CHH_OB_SRR389222_sub1_bismark_bt2.txt.gz:md5,12e9e4ebf59e6b23fb52f4872f534251",
+                        "CHH_OT_SRR389222_sub1_bismark_bt2.txt.gz:md5,b800b59b0987650ac6eb4d2eb25451ad",
+                        "CpG_OB_SRR389222_sub1_bismark_bt2.txt.gz:md5,21d614f45ecf703117550cb2eebfa3d5",
+                        "CpG_OT_SRR389222_sub1_bismark_bt2.txt.gz:md5,8bbe9103623f502908e81cc573754524"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_bt2.bismark.cov.gz:md5,4e31b9a432731c75a604c89cb9d471ad"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_bt2_splitting_report.txt:md5,d1bc9da2811d0f20981d01c3b1f4c925"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_bt2.M-bias.txt:md5,d1083f305a444487fe977362a0174159"
+                ]
+            ],
+            [
+                "SRR389222_sub1_bismark_bt2_SE_report.html"
+            ],
+            "bismark_summary_report.txt:md5,13f7305cf7003f54e0eba22f3590889a",
+            [
+                "SRR389222_sub1_bismark_bt2.M-bias.txt",
+                "SRR389222_sub1_bismark_bt2_SE_report.html",
+                "SRR389222_sub1_bismark_bt2_SE_report.txt",
+                "SRR389222_sub1_bismark_bt2_splitting_report.txt",
+                "bismark_summary_report.html",
+                "bismark_summary_report.txt"
+            ],
+            [
+                "versions.yml:md5,46e043d0037e7446544ae1e25b65536c",
+                "versions.yml:md5,6c516cc03aa69228e503c540ee3794aa",
+                "versions.yml:md5,6f2f867f534bb0ae0ffbdc52d036afce",
+                "versions.yml:md5,9b480db277eebeb6265cbd003553c22c",
+                "versions.yml:md5,aa64d431e6cfc5ffcbd5012a76b0c1a3",
+                "versions.yml:md5,df1a6bcb24960ee4a22a2cc914c65272"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-15T15:19:32.095795684"
+    },
+    "Params: bismark | default": {
+        "content": [
+            [
+                
+            ],
+            [
+                "test.sorted.bam.bai"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_bt2.deduplicated.bedGraph.gz:md5,5d7312489e51ca88e1ce1f689db93a64"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    [
+                        "CHG_OB_SRR389222_sub1_bismark_bt2.deduplicated.txt.gz:md5,5c177e6f00dfc6e2335a55c6b70efa0c",
+                        "CHG_OT_SRR389222_sub1_bismark_bt2.deduplicated.txt.gz:md5,5362d479358f644fe2c17cfe02f310f8",
+                        "CHH_OB_SRR389222_sub1_bismark_bt2.deduplicated.txt.gz:md5,9469ac28e4369032b855ce1a794a56a4",
+                        "CHH_OT_SRR389222_sub1_bismark_bt2.deduplicated.txt.gz:md5,d7628ac941d3fea97297a8dfcfb7aed1",
+                        "CpG_OB_SRR389222_sub1_bismark_bt2.deduplicated.txt.gz:md5,f0404fc1fc18c7ff58e8766b405239ed",
+                        "CpG_OT_SRR389222_sub1_bismark_bt2.deduplicated.txt.gz:md5,67d04d843e9e1abc8643bc25b27a9ff5"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_bt2.deduplicated.bismark.cov.gz:md5,eb0d3f96ed97c5d12afeeb49c234849d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_bt2.deduplicated_splitting_report.txt:md5,ec268cc572b8bcfea0959b47c7510f05"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_bt2.deduplicated.M-bias.txt:md5,290ebfeca4da7809cf9adfe60bab1b29"
+                ]
+            ],
+            [
+                "SRR389222_sub1_bismark_bt2_SE_report.html"
+            ],
+            "bismark_summary_report.txt:md5,46f54eec58516c027e20bc9bdcaaae14",
+            [
+                "SRR389222_sub1_bismark_bt2.deduplicated.M-bias.txt",
+                "SRR389222_sub1_bismark_bt2.deduplicated_splitting_report.txt",
+                "SRR389222_sub1_bismark_bt2.deduplication_report.txt",
+                "SRR389222_sub1_bismark_bt2_SE_report.html",
+                "SRR389222_sub1_bismark_bt2_SE_report.txt",
+                "bismark_summary_report.html",
+                "bismark_summary_report.txt"
+            ],
+            [
+                "versions.yml:md5,46e043d0037e7446544ae1e25b65536c",
+                "versions.yml:md5,6c516cc03aa69228e503c540ee3794aa",
+                "versions.yml:md5,6f2f867f534bb0ae0ffbdc52d036afce",
+                "versions.yml:md5,9b480db277eebeb6265cbd003553c22c",
+                "versions.yml:md5,a675051417ba65700b5db32d98aa65b6",
+                "versions.yml:md5,aa64d431e6cfc5ffcbd5012a76b0c1a3",
+                "versions.yml:md5,df1a6bcb24960ee4a22a2cc914c65272"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-15T15:18:51.250132036"
+    },
+    "Params: bismark | cytosine_report": {
+        "content": [
+            [
+                
+            ],
+            [
+                "test.sorted.bam.bai"
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.CpG_report.txt.gz:md5,33af7ef6af01da4f1e12457ff1d782c6"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.cytosine_context_summary.txt:md5,0e8c65559470bc64c42dbd0278a531de"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_bt2.deduplicated.bedGraph.gz:md5,5d7312489e51ca88e1ce1f689db93a64"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    [
+                        "CHG_OB_SRR389222_sub1_bismark_bt2.deduplicated.txt.gz:md5,5c177e6f00dfc6e2335a55c6b70efa0c",
+                        "CHG_OT_SRR389222_sub1_bismark_bt2.deduplicated.txt.gz:md5,5362d479358f644fe2c17cfe02f310f8",
+                        "CHH_OB_SRR389222_sub1_bismark_bt2.deduplicated.txt.gz:md5,9469ac28e4369032b855ce1a794a56a4",
+                        "CHH_OT_SRR389222_sub1_bismark_bt2.deduplicated.txt.gz:md5,d7628ac941d3fea97297a8dfcfb7aed1",
+                        "CpG_OB_SRR389222_sub1_bismark_bt2.deduplicated.txt.gz:md5,f0404fc1fc18c7ff58e8766b405239ed",
+                        "CpG_OT_SRR389222_sub1_bismark_bt2.deduplicated.txt.gz:md5,67d04d843e9e1abc8643bc25b27a9ff5"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_bt2.deduplicated.bismark.cov.gz:md5,eb0d3f96ed97c5d12afeeb49c234849d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_bt2.deduplicated_splitting_report.txt:md5,ec268cc572b8bcfea0959b47c7510f05"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_bt2.deduplicated.M-bias.txt:md5,290ebfeca4da7809cf9adfe60bab1b29"
+                ]
+            ],
+            [
+                "SRR389222_sub1_bismark_bt2_SE_report.html"
+            ],
+            "bismark_summary_report.txt:md5,46f54eec58516c027e20bc9bdcaaae14",
+            [
+                "SRR389222_sub1_bismark_bt2.deduplicated.M-bias.txt",
+                "SRR389222_sub1_bismark_bt2.deduplicated_splitting_report.txt",
+                "SRR389222_sub1_bismark_bt2.deduplication_report.txt",
+                "SRR389222_sub1_bismark_bt2_SE_report.html",
+                "SRR389222_sub1_bismark_bt2_SE_report.txt",
+                "bismark_summary_report.html",
+                "bismark_summary_report.txt"
+            ],
+            [
+                "versions.yml:md5,46e043d0037e7446544ae1e25b65536c",
+                "versions.yml:md5,6c516cc03aa69228e503c540ee3794aa",
+                "versions.yml:md5,6f2f867f534bb0ae0ffbdc52d036afce",
+                "versions.yml:md5,9b480db277eebeb6265cbd003553c22c",
+                "versions.yml:md5,a675051417ba65700b5db32d98aa65b6",
+                "versions.yml:md5,aa64d431e6cfc5ffcbd5012a76b0c1a3",
+                "versions.yml:md5,df1a6bcb24960ee4a22a2cc914c65272",
+                "versions.yml:md5,eb23ca81cb3427b8c5a8a9a93def4882"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-15T15:20:14.052464546"
+    },
+    "Params: bismark_hisat | cytosine_report": {
+        "content": [
+            [
+                
+            ],
+            [
+                "test.sorted.bam.bai"
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.CpG_report.txt.gz:md5,d05837f07e4866f007d1f25166376b10"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "test.cytosine_context_summary.txt:md5,c2e99c47feb351c6666990bec7d1a9bd"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_hisat2.deduplicated.bedGraph.gz:md5,1f1b14f7be535e6098ece13ea1406bfc"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    [
+                        "CHG_OB_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,5c177e6f00dfc6e2335a55c6b70efa0c",
+                        "CHG_OT_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,138bccceb9ae71ecdae6828fd8fc327f",
+                        "CHH_OB_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,9469ac28e4369032b855ce1a794a56a4",
+                        "CHH_OT_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,f1acfc10c9f9ffb80f2a7a947a210ad7",
+                        "CpG_OB_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,f0404fc1fc18c7ff58e8766b405239ed",
+                        "CpG_OT_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,75b9acaf689411154f906bcfa7264abf"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_hisat2.deduplicated.bismark.cov.gz:md5,ec4a2575b47822ef478b3bda35c70590"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_hisat2.deduplicated_splitting_report.txt:md5,eaee004ea3fffb9b8aaf968f41f9f903"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_hisat2.deduplicated.M-bias.txt:md5,82b760a6824f55f6732297374d77a6ec"
+                ]
+            ],
+            [
+                "SRR389222_sub1_bismark_hisat2_SE_report.html"
+            ],
+            "bismark_summary_report.txt:md5,762c303acee29bfffef35b3d9e04d153",
+            [
+                "SRR389222_sub1_bismark_hisat2.deduplicated.M-bias.txt",
+                "SRR389222_sub1_bismark_hisat2.deduplicated_splitting_report.txt",
+                "SRR389222_sub1_bismark_hisat2.deduplication_report.txt",
+                "SRR389222_sub1_bismark_hisat2_SE_report.html",
+                "SRR389222_sub1_bismark_hisat2_SE_report.txt",
+                "bismark_summary_report.html",
+                "bismark_summary_report.txt"
+            ],
+            [
+                "versions.yml:md5,46e043d0037e7446544ae1e25b65536c",
+                "versions.yml:md5,6c516cc03aa69228e503c540ee3794aa",
+                "versions.yml:md5,6f2f867f534bb0ae0ffbdc52d036afce",
+                "versions.yml:md5,9b480db277eebeb6265cbd003553c22c",
+                "versions.yml:md5,a675051417ba65700b5db32d98aa65b6",
+                "versions.yml:md5,aa64d431e6cfc5ffcbd5012a76b0c1a3",
+                "versions.yml:md5,df1a6bcb24960ee4a22a2cc914c65272",
+                "versions.yml:md5,eb23ca81cb3427b8c5a8a9a93def4882"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-15T15:22:14.454171707"
+    },
+    "Params: bismark_hisat | default": {
+        "content": [
+            [
+                
+            ],
+            [
+                "test.sorted.bam.bai"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_hisat2.deduplicated.bedGraph.gz:md5,1f1b14f7be535e6098ece13ea1406bfc"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    [
+                        "CHG_OB_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,5c177e6f00dfc6e2335a55c6b70efa0c",
+                        "CHG_OT_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,138bccceb9ae71ecdae6828fd8fc327f",
+                        "CHH_OB_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,9469ac28e4369032b855ce1a794a56a4",
+                        "CHH_OT_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,f1acfc10c9f9ffb80f2a7a947a210ad7",
+                        "CpG_OB_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,f0404fc1fc18c7ff58e8766b405239ed",
+                        "CpG_OT_SRR389222_sub1_bismark_hisat2.deduplicated.txt.gz:md5,75b9acaf689411154f906bcfa7264abf"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_hisat2.deduplicated.bismark.cov.gz:md5,ec4a2575b47822ef478b3bda35c70590"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_hisat2.deduplicated_splitting_report.txt:md5,eaee004ea3fffb9b8aaf968f41f9f903"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_hisat2.deduplicated.M-bias.txt:md5,82b760a6824f55f6732297374d77a6ec"
+                ]
+            ],
+            [
+                "SRR389222_sub1_bismark_hisat2_SE_report.html"
+            ],
+            "bismark_summary_report.txt:md5,762c303acee29bfffef35b3d9e04d153",
+            [
+                "SRR389222_sub1_bismark_hisat2.deduplicated.M-bias.txt",
+                "SRR389222_sub1_bismark_hisat2.deduplicated_splitting_report.txt",
+                "SRR389222_sub1_bismark_hisat2.deduplication_report.txt",
+                "SRR389222_sub1_bismark_hisat2_SE_report.html",
+                "SRR389222_sub1_bismark_hisat2_SE_report.txt",
+                "bismark_summary_report.html",
+                "bismark_summary_report.txt"
+            ],
+            [
+                "versions.yml:md5,46e043d0037e7446544ae1e25b65536c",
+                "versions.yml:md5,6c516cc03aa69228e503c540ee3794aa",
+                "versions.yml:md5,6f2f867f534bb0ae0ffbdc52d036afce",
+                "versions.yml:md5,9b480db277eebeb6265cbd003553c22c",
+                "versions.yml:md5,a675051417ba65700b5db32d98aa65b6",
+                "versions.yml:md5,aa64d431e6cfc5ffcbd5012a76b0c1a3",
+                "versions.yml:md5,df1a6bcb24960ee4a22a2cc914c65272"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-15T15:20:53.556708293"
+    },
+    "Params: bismark_hisat | skip_deduplication": {
+        "content": [
+            [
+                
+            ],
+            [
+                "test.sorted.bam.bai"
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_hisat2.bedGraph.gz:md5,75be0d8be0134a48fd55e15a49568d3f"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    [
+                        "CHG_OB_SRR389222_sub1_bismark_hisat2.txt.gz:md5,11ae58ebe6513375468ebe63a521d6e3",
+                        "CHG_OT_SRR389222_sub1_bismark_hisat2.txt.gz:md5,2963a2702be660068818073a2989c790",
+                        "CHH_OB_SRR389222_sub1_bismark_hisat2.txt.gz:md5,12e9e4ebf59e6b23fb52f4872f534251",
+                        "CHH_OT_SRR389222_sub1_bismark_hisat2.txt.gz:md5,e6815f62702d06dc01d12ea18dbd9a03",
+                        "CpG_OB_SRR389222_sub1_bismark_hisat2.txt.gz:md5,21d614f45ecf703117550cb2eebfa3d5",
+                        "CpG_OT_SRR389222_sub1_bismark_hisat2.txt.gz:md5,1a07c82f278b4ed637d33833df1e9749"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_hisat2.bismark.cov.gz:md5,ab610e006112a52e5ecb230a1704f236"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_hisat2_splitting_report.txt:md5,e6b01d28d7248361750dbd23eef667df"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": true
+                    },
+                    "SRR389222_sub1_bismark_hisat2.M-bias.txt:md5,bbfe49763c571a55a50d1e46c0fb4e46"
+                ]
+            ],
+            [
+                "SRR389222_sub1_bismark_hisat2_SE_report.html"
+            ],
+            "bismark_summary_report.txt:md5,7a466655c11944b6035901910378e559",
+            [
+                "SRR389222_sub1_bismark_hisat2.M-bias.txt",
+                "SRR389222_sub1_bismark_hisat2_SE_report.html",
+                "SRR389222_sub1_bismark_hisat2_SE_report.txt",
+                "SRR389222_sub1_bismark_hisat2_splitting_report.txt",
+                "bismark_summary_report.html",
+                "bismark_summary_report.txt"
+            ],
+            [
+                "versions.yml:md5,46e043d0037e7446544ae1e25b65536c",
+                "versions.yml:md5,6c516cc03aa69228e503c540ee3794aa",
+                "versions.yml:md5,6f2f867f534bb0ae0ffbdc52d036afce",
+                "versions.yml:md5,9b480db277eebeb6265cbd003553c22c",
+                "versions.yml:md5,aa64d431e6cfc5ffcbd5012a76b0c1a3",
+                "versions.yml:md5,df1a6bcb24960ee4a22a2cc914c65272"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-15T15:21:33.809590706"
+    }
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_align_dedup_bismark/tests/nextflow.config b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/nextflow.config
new file mode 100644
index 00000000000..903bb19fa88
--- /dev/null
+++ b/subworkflows/nf-core/fastq_align_dedup_bismark/tests/nextflow.config
@@ -0,0 +1,15 @@
+params {
+    aligner            = "bismark"
+    cytosine_report    = false
+    skip_deduplication = false
+}
+
+process {
+    withName: 'BISMARK_ALIGN' {
+            ext.args = { params.aligner == 'bismark_hisat' ? ' --hisat2' : ' --bowtie2' }
+    }
+
+    withName: 'SAMTOOLS_SORT_DEDUPLICATED' {
+        ext.prefix = { "${meta.id}.sorted" }
+    }
+}

From 7ed0aec1b50be96284fb7526ce79ae54d4f5f2ed Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Sat, 16 Nov 2024 13:27:19 +0000
Subject: [PATCH 11/12] chore(deps): pin dependencies (#7004)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
---
 .github/actions/nf-test-action/action.yml | 4 ++--
 .github/workflows/test.yml                | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/actions/nf-test-action/action.yml b/.github/actions/nf-test-action/action.yml
index 4dd6df48919..e1e1f4bc57d 100644
--- a/.github/actions/nf-test-action/action.yml
+++ b/.github/actions/nf-test-action/action.yml
@@ -11,9 +11,9 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-    - uses: actions/setup-java@v4
+    - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
       with:
         distribution: "temurin"
         java-version: "17"
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 0ff73656067..736b2c9eae9 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -88,7 +88,7 @@ jobs:
         with:
           fetch-depth: 2 # To retrieve the preceding commit.
 
-      - uses: dorny/paths-filter@v3
+      - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3
         id: filter
         with:
           filters: "tests/config/pytest_modules.yml"

From 8ad72fdac2212c9e84b6187e85b9cefb507d1575 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Famke=20Ba=CC=88uerle?= <famke.baeuerle@gmail.com>
Date: Mon, 18 Nov 2024 11:19:41 +0100
Subject: [PATCH 12/12] update test yaml

---
 .github/workflows/test.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 736b2c9eae9..a2ba0b53a62 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -662,6 +662,7 @@ jobs:
           - path: modules/nf-core/parabricks/fq2bammeth
           - path: modules/nf-core/parabricks/fq2bam
           - path: modules/nf-core/parabricks/applybqsr
+          - path: modules/nf-core/parabricks/indexgvcf
           - profile: conda
             path: modules/nf-core/xeniumranger/relabel
           - profile: conda
@@ -698,6 +699,8 @@ jobs:
             profile: [docker_self_hosted, singularity]
           - path: modules/nf-core/parabricks/fq2bammeth
             profile: [docker_self_hosted, singularity]
+          - path: modules/nf-core/parabricks/indexgvcf
+            profile: [docker_self_hosted, singularity]
     env:
       NXF_ANSI_LOG: false