From 0084d3e21eaa37fd61b56546b6bdadf9e956ad1c Mon Sep 17 00:00:00 2001
From: Lucas <lpatel@ucsd.edu>
Date: Wed, 14 Jan 2026 10:55:23 -0800
Subject: [PATCH 1/4] feat: Added ViralConsensus module

---
 .../nf-core/viralconsensus/environment.yml    |   8 ++
 modules/nf-core/viralconsensus/main.nf        |  50 ++++++++
 modules/nf-core/viralconsensus/meta.yml       | 113 +++++++++++++++++
 .../nf-core/viralconsensus/tests/main.nf.test | 115 +++++++++++++++++
 .../viralconsensus/tests/main.nf.test.snap    | 119 ++++++++++++++++++
 .../viralconsensus/tests/nextflow.config      |   5 +
 .../tests/nextflow_optional.config            |   7 ++
 7 files changed, 417 insertions(+)
 create mode 100644 modules/nf-core/viralconsensus/environment.yml
 create mode 100644 modules/nf-core/viralconsensus/main.nf
 create mode 100644 modules/nf-core/viralconsensus/meta.yml
 create mode 100644 modules/nf-core/viralconsensus/tests/main.nf.test
 create mode 100644 modules/nf-core/viralconsensus/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/viralconsensus/tests/nextflow.config
 create mode 100644 modules/nf-core/viralconsensus/tests/nextflow_optional.config

diff --git a/modules/nf-core/viralconsensus/environment.yml b/modules/nf-core/viralconsensus/environment.yml
new file mode 100644
index 000000000000..390707db5d97
--- /dev/null
+++ b/modules/nf-core/viralconsensus/environment.yml
@@ -0,0 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # renovate: datasource=conda depName=bioconda/viral_consensus
+  - bioconda::viral_consensus=1.0.0
diff --git a/modules/nf-core/viralconsensus/main.nf b/modules/nf-core/viralconsensus/main.nf
new file mode 100644
index 000000000000..b34420ba7cbd
--- /dev/null
+++ b/modules/nf-core/viralconsensus/main.nf
@@ -0,0 +1,50 @@
+process VIRALCONSENSUS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/viral_consensus:1.0.0--hcf1f8c1_0':
+        'biocontainers/viral_consensus:1.0.0--hcf1f8c1_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+    path fasta
+    path primer_bed
+
+    output:
+    tuple val(meta), path("*.consensus.fa"), emit: fasta
+    tuple val(meta), path("*.pos_counts.tsv"), optional: true, emit: pos_counts
+    tuple val(meta), path("*.ins_counts.json"), optional: true, emit: ins_counts
+    tuple val("${task.process}"), val('viralconsensus'), eval("viral_consensus --version 2>&1 | head -n1 | sed 's/ViralConsensus //'"), topic: versions, emit: versions_viralconsensus
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def primer_arg = primer_bed ? "-p ${primer_bed}" : ''
+    def pos_counts_arg = task.ext.save_pos_counts ? "-op ${prefix}.pos_counts.tsv" : ''
+    def ins_counts_arg = task.ext.save_ins_counts ? "-oi ${prefix}.ins_counts.json" : ''
+    """
+    viral_consensus \\
+        -i $bam \\
+        -r $fasta \\
+        -o ${prefix}.consensus.fa \\
+        $primer_arg \\
+        $pos_counts_arg \\
+        $ins_counts_arg \\
+        $args
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def touch_pos_counts = task.ext.save_pos_counts ? "touch ${prefix}.pos_counts.tsv" : ''
+    def touch_ins_counts = task.ext.save_ins_counts ? "touch ${prefix}.ins_counts.json" : ''
+    """
+    touch ${prefix}.consensus.fa
+    $touch_pos_counts
+    $touch_ins_counts
+    """
+}
diff --git a/modules/nf-core/viralconsensus/meta.yml b/modules/nf-core/viralconsensus/meta.yml
new file mode 100644
index 000000000000..99ab0cb9dc99
--- /dev/null
+++ b/modules/nf-core/viralconsensus/meta.yml
@@ -0,0 +1,113 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "viralconsensus"
+description: Fast and memory-efficient viral consensus genome sequence
+  generation from read alignments
+keywords:
+  - virus
+  - genomics
+  - consensus
+  - bam
+  - fasta
+tools:
+  - "viralconsensus":
+      description: "ViralConsensus is a fast and memory-efficient tool for calling viral
+        consensus genome sequences directly from read alignment data."
+      homepage: "https://github.com/niemasd/ViralConsensus"
+      documentation: "https://github.com/niemasd/ViralConsensus#usage"
+      tool_dev_url: "https://github.com/niemasd/ViralConsensus"
+      doi: "10.1093/bioinformatics/btad317"
+      licence: ["GPL-3.0-or-later"]
+      identifier: biotools:viralconsensus
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM/SAM/CRAM file containing aligned reads
+        pattern: "*.{bam,sam,cram}"
+        ontologies:
+          - edam: http://edamontology.org/format_2572
+  - fasta:
+      type: file
+      description: Reference genome sequence in FASTA format
+      pattern: "*.{fa,fasta,fna}"
+      ontologies:
+        - edam: http://edamontology.org/format_1929
+  - primer_bed:
+      type: file
+      description: Optional BED file with primer coordinates for trimming
+      pattern: "*.bed"
+      ontologies:
+        - edam: http://edamontology.org/format_3003
+
+output:
+  fasta:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.consensus.fa":
+          type: file
+          description: Consensus genome sequence in FASTA format
+          pattern: "*.consensus.fa"
+          ontologies:
+            - edam: http://edamontology.org/format_1929
+  pos_counts:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.pos_counts.tsv":
+          type: file
+          description: Per-position base counts (optional, enabled via
+            task.ext.save_pos_counts)
+          pattern: "*.pos_counts.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475
+  ins_counts:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.ins_counts.json":
+          type: file
+          description: Insertion counts (optional, enabled via
+            task.ext.save_ins_counts)
+          pattern: "*.ins_counts.json"
+          ontologies:
+            - edam: http://edamontology.org/format_3464
+  versions_viralconsensus:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - viralconsensus:
+          type: string
+          description: The name of the tool
+      - "viral_consensus --version 2>&1 | head -n1 | sed 's/ViralConsensus //'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - viralconsensus:
+          type: string
+          description: The name of the tool
+      - "viral_consensus --version 2>&1 | head -n1 | sed 's/ViralConsensus //'":
+          type: eval
+          description: The expression to obtain the version of the tool
+
+authors:
+  - "@niemasd"
+maintainers:
+  - "@niemasd"
+  - "@lucaspatel"
diff --git a/modules/nf-core/viralconsensus/tests/main.nf.test b/modules/nf-core/viralconsensus/tests/main.nf.test
new file mode 100644
index 000000000000..4f5a19b480d0
--- /dev/null
+++ b/modules/nf-core/viralconsensus/tests/main.nf.test
@@ -0,0 +1,115 @@
+nextflow_process {
+
+    name "Test Process VIRALCONSENSUS"
+    script "../main.nf"
+    process "VIRALCONSENSUS"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "viralconsensus"
+
+    test("sarscov2 - bam - basic") {
+
+        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] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.fasta,
+                    process.out.versions_viralconsensus
+                ).match("basic") }
+            )
+        }
+    }
+
+    test("sarscov2 - bam - with primer bed") {
+
+        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] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.fasta,
+                    process.out.versions_viralconsensus
+                ).match("primer") }
+            )
+        }
+    }
+
+    test("sarscov2 - bam - with optional outputs") {
+
+        config "./nextflow_optional.config"
+
+        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] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.fasta },
+                { assert process.out.pos_counts },
+                { assert process.out.ins_counts },
+                { assert snapshot(process.out.versions_viralconsensus).match("optional_versions") }
+            )
+        }
+    }
+
+    test("sarscov2 - bam - 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] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match("stub") }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/viralconsensus/tests/main.nf.test.snap b/modules/nf-core/viralconsensus/tests/main.nf.test.snap
new file mode 100644
index 000000000000..c4c2333dd35a
--- /dev/null
+++ b/modules/nf-core/viralconsensus/tests/main.nf.test.snap
@@ -0,0 +1,119 @@
+{
+    "optional_versions": {
+        "content": [
+            [
+                [
+                    "VIRALCONSENSUS",
+                    "viralconsensus",
+                    "viral_consensus v1.0.0"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-01-13T15:28:13.237078"
+    },
+    "primer": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.consensus.fa:md5,67220b967a5ebe4827f1ff418fd73654"
+                ]
+            ],
+            [
+                [
+                    "VIRALCONSENSUS",
+                    "viralconsensus",
+                    "viral_consensus v1.0.0"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-01-13T15:28:02.876743"
+    },
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.consensus.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    [
+                        "VIRALCONSENSUS",
+                        "viralconsensus",
+                        "viral_consensus v1.0.0"
+                    ]
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.consensus.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "ins_counts": [
+                    
+                ],
+                "pos_counts": [
+                    
+                ],
+                "versions_viralconsensus": [
+                    [
+                        "VIRALCONSENSUS",
+                        "viralconsensus",
+                        "viral_consensus v1.0.0"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-01-13T15:27:00.993246"
+    },
+    "basic": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.consensus.fa:md5,c1a43a011177eff31a4afa9fb8612c7b"
+                ]
+            ],
+            [
+                [
+                    "VIRALCONSENSUS",
+                    "viralconsensus",
+                    "viral_consensus v1.0.0"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-01-13T15:27:52.452933"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/viralconsensus/tests/nextflow.config b/modules/nf-core/viralconsensus/tests/nextflow.config
new file mode 100644
index 000000000000..e221518b52da
--- /dev/null
+++ b/modules/nf-core/viralconsensus/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: VIRALCONSENSUS {
+        ext.args = '-q 20 -d 10 -f 0.5'
+    }
+}
diff --git a/modules/nf-core/viralconsensus/tests/nextflow_optional.config b/modules/nf-core/viralconsensus/tests/nextflow_optional.config
new file mode 100644
index 000000000000..35913a26f371
--- /dev/null
+++ b/modules/nf-core/viralconsensus/tests/nextflow_optional.config
@@ -0,0 +1,7 @@
+process {
+    withName: VIRALCONSENSUS {
+        ext.args = '-q 20 -d 10 -f 0.5'
+        ext.save_pos_counts = true
+        ext.save_ins_counts = true
+    }
+}

From 21f2c121bce5a0d56bcf26dcccafcea77ef52963 Mon Sep 17 00:00:00 2001
From: Lucas <lpatel@ucsd.edu>
Date: Wed, 14 Jan 2026 15:26:09 -0800
Subject: [PATCH 2/4] fix: update test snapshots for Docker compatibility

---
 modules/nf-core/viralconsensus/tests/main.nf.test.snap | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/viralconsensus/tests/main.nf.test.snap b/modules/nf-core/viralconsensus/tests/main.nf.test.snap
index c4c2333dd35a..005c4a40bda9 100644
--- a/modules/nf-core/viralconsensus/tests/main.nf.test.snap
+++ b/modules/nf-core/viralconsensus/tests/main.nf.test.snap
@@ -13,7 +13,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-13T15:28:13.237078"
+        "timestamp": "2026-01-14T15:23:45.652845"
     },
     "primer": {
         "content": [
@@ -37,7 +37,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-13T15:28:02.876743"
+        "timestamp": "2026-01-14T15:23:40.272776"
     },
     "stub": {
         "content": [
@@ -90,7 +90,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-13T15:27:00.993246"
+        "timestamp": "2026-01-14T15:23:48.828319"
     },
     "basic": {
         "content": [
@@ -114,6 +114,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-13T15:27:52.452933"
+        "timestamp": "2026-01-14T15:23:36.859097"
     }
 }
\ No newline at end of file

From 745fdb3934455763a998a5ac08598b3c2467e1e9 Mon Sep 17 00:00:00 2001
From: Lucas <lpatel@ucsd.edu>
Date: Sat, 24 Jan 2026 19:43:56 -0800
Subject: [PATCH 3/4] fix: task.ext to optional inputs

---
 modules/nf-core/viralconsensus/main.nf               | 10 ++++++----
 modules/nf-core/viralconsensus/meta.yml              | 12 ++++++++++--
 modules/nf-core/viralconsensus/tests/main.nf.test    |  8 ++++++++
 .../viralconsensus/tests/nextflow_optional.config    |  2 --
 4 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/modules/nf-core/viralconsensus/main.nf b/modules/nf-core/viralconsensus/main.nf
index b34420ba7cbd..e43ade1ba205 100644
--- a/modules/nf-core/viralconsensus/main.nf
+++ b/modules/nf-core/viralconsensus/main.nf
@@ -11,6 +11,8 @@ process VIRALCONSENSUS {
     tuple val(meta), path(bam)
     path fasta
     path primer_bed
+    val save_pos_counts
+    val save_ins_counts
 
     output:
     tuple val(meta), path("*.consensus.fa"), emit: fasta
@@ -25,8 +27,8 @@ process VIRALCONSENSUS {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def primer_arg = primer_bed ? "-p ${primer_bed}" : ''
-    def pos_counts_arg = task.ext.save_pos_counts ? "-op ${prefix}.pos_counts.tsv" : ''
-    def ins_counts_arg = task.ext.save_ins_counts ? "-oi ${prefix}.ins_counts.json" : ''
+    def pos_counts_arg = save_pos_counts ? "-op ${prefix}.pos_counts.tsv" : ''
+    def ins_counts_arg = save_ins_counts ? "-oi ${prefix}.ins_counts.json" : ''
     """
     viral_consensus \\
         -i $bam \\
@@ -40,8 +42,8 @@ process VIRALCONSENSUS {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def touch_pos_counts = task.ext.save_pos_counts ? "touch ${prefix}.pos_counts.tsv" : ''
-    def touch_ins_counts = task.ext.save_ins_counts ? "touch ${prefix}.ins_counts.json" : ''
+    def touch_pos_counts = save_pos_counts ? "touch ${prefix}.pos_counts.tsv" : ''
+    def touch_ins_counts = save_ins_counts ? "touch ${prefix}.ins_counts.json" : ''
     """
     touch ${prefix}.consensus.fa
     $touch_pos_counts
diff --git a/modules/nf-core/viralconsensus/meta.yml b/modules/nf-core/viralconsensus/meta.yml
index 99ab0cb9dc99..092740eb7971 100644
--- a/modules/nf-core/viralconsensus/meta.yml
+++ b/modules/nf-core/viralconsensus/meta.yml
@@ -43,6 +43,14 @@ input:
       pattern: "*.bed"
       ontologies:
         - edam: http://edamontology.org/format_3003
+  - save_pos_counts:
+      type: boolean
+      description: |
+        Save per-position counts to a TSV file
+  - save_ins_counts:
+      type: boolean
+      description: |
+        Save insertion counts to a JSON file
 
 output:
   fasta:
@@ -66,7 +74,7 @@ output:
       - "*.pos_counts.tsv":
           type: file
           description: Per-position base counts (optional, enabled via
-            task.ext.save_pos_counts)
+            save_pos_counts input)
           pattern: "*.pos_counts.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475
@@ -79,7 +87,7 @@ output:
       - "*.ins_counts.json":
           type: file
           description: Insertion counts (optional, enabled via
-            task.ext.save_ins_counts)
+            save_ins_counts input)
           pattern: "*.ins_counts.json"
           ontologies:
             - edam: http://edamontology.org/format_3464
diff --git a/modules/nf-core/viralconsensus/tests/main.nf.test b/modules/nf-core/viralconsensus/tests/main.nf.test
index 4f5a19b480d0..378052169f4c 100644
--- a/modules/nf-core/viralconsensus/tests/main.nf.test
+++ b/modules/nf-core/viralconsensus/tests/main.nf.test
@@ -20,6 +20,8 @@ nextflow_process {
                 ]
                 input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 input[2] = []
+                input[3] = false
+                input[4] = false
                 """
             }
         }
@@ -46,6 +48,8 @@ nextflow_process {
                 ]
                 input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                input[3] = false
+                input[4] = false
                 """
             }
         }
@@ -74,6 +78,8 @@ nextflow_process {
                 ]
                 input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 input[2] = []
+                input[3] = true
+                input[4] = true
                 """
             }
         }
@@ -101,6 +107,8 @@ nextflow_process {
                 ]
                 input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 input[2] = []
+                input[3] = false
+                input[4] = false
                 """
             }
         }
diff --git a/modules/nf-core/viralconsensus/tests/nextflow_optional.config b/modules/nf-core/viralconsensus/tests/nextflow_optional.config
index 35913a26f371..e221518b52da 100644
--- a/modules/nf-core/viralconsensus/tests/nextflow_optional.config
+++ b/modules/nf-core/viralconsensus/tests/nextflow_optional.config
@@ -1,7 +1,5 @@
 process {
     withName: VIRALCONSENSUS {
         ext.args = '-q 20 -d 10 -f 0.5'
-        ext.save_pos_counts = true
-        ext.save_ins_counts = true
     }
 }

From 8a5fd20ea7d752eece84fdc957095bc6bd77f5b3 Mon Sep 17 00:00:00 2001
From: Lucas <lpatel@ucsd.edu>
Date: Sat, 24 Jan 2026 19:58:17 -0800
Subject: [PATCH 4/4] fix: update configuration of ext.args in tests

---
 .../nf-core/viralconsensus/tests/main.nf.test |  26 ++--
 .../viralconsensus/tests/main.nf.test.snap    | 126 +++++++++++-------
 .../viralconsensus/tests/nextflow.config      |   2 +-
 .../tests/nextflow_optional.config            |   5 -
 4 files changed, 94 insertions(+), 65 deletions(-)
 delete mode 100644 modules/nf-core/viralconsensus/tests/nextflow_optional.config

diff --git a/modules/nf-core/viralconsensus/tests/main.nf.test b/modules/nf-core/viralconsensus/tests/main.nf.test
index 378052169f4c..ea4a46743607 100644
--- a/modules/nf-core/viralconsensus/tests/main.nf.test
+++ b/modules/nf-core/viralconsensus/tests/main.nf.test
@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process VIRALCONSENSUS"
     script "../main.nf"
     process "VIRALCONSENSUS"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -31,8 +30,8 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.fasta,
-                    process.out.versions_viralconsensus
-                ).match("basic") }
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
             )
         }
     }
@@ -59,17 +58,20 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.fasta,
-                    process.out.versions_viralconsensus
-                ).match("primer") }
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
             )
         }
     }
 
     test("sarscov2 - bam - with optional outputs") {
 
-        config "./nextflow_optional.config"
+        config "./nextflow.config"
 
         when {
+            params {
+                module_args = '-q 30 -d 5 -f 0.6'
+            }
             process {
                 """
                 input[0] = [
@@ -87,10 +89,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert process.out.fasta },
-                { assert process.out.pos_counts },
-                { assert process.out.ins_counts },
-                { assert snapshot(process.out.versions_viralconsensus).match("optional_versions") }
+                { assert snapshot(
+                    process.out.fasta,
+                    process.out.pos_counts,
+                    process.out.ins_counts,
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
             )
         }
     }
@@ -116,7 +120,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("stub") }
+                { assert snapshot(process.out).match() }
             )
         }
     }
diff --git a/modules/nf-core/viralconsensus/tests/main.nf.test.snap b/modules/nf-core/viralconsensus/tests/main.nf.test.snap
index 005c4a40bda9..a114903ecd92 100644
--- a/modules/nf-core/viralconsensus/tests/main.nf.test.snap
+++ b/modules/nf-core/viralconsensus/tests/main.nf.test.snap
@@ -1,45 +1,5 @@
 {
-    "optional_versions": {
-        "content": [
-            [
-                [
-                    "VIRALCONSENSUS",
-                    "viralconsensus",
-                    "viral_consensus v1.0.0"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-14T15:23:45.652845"
-    },
-    "primer": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.consensus.fa:md5,67220b967a5ebe4827f1ff418fd73654"
-                ]
-            ],
-            [
-                [
-                    "VIRALCONSENSUS",
-                    "viralconsensus",
-                    "viral_consensus v1.0.0"
-                ]
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-14T15:23:40.272776"
-    },
-    "stub": {
+    "sarscov2 - bam - stub": {
         "content": [
             {
                 "0": [
@@ -90,9 +50,35 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-14T15:23:48.828319"
+        "timestamp": "2026-01-24T19:54:20.412415"
     },
-    "basic": {
+    "sarscov2 - bam - with primer bed": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.consensus.fa:md5,67220b967a5ebe4827f1ff418fd73654"
+                ]
+            ],
+            {
+                "versions_viralconsensus": [
+                    [
+                        "VIRALCONSENSUS",
+                        "viralconsensus",
+                        "viral_consensus v1.0.0"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-01-24T19:56:36.892682"
+    },
+    "sarscov2 - bam - basic": {
         "content": [
             [
                 [
@@ -102,18 +88,62 @@
                     "test.consensus.fa:md5,c1a43a011177eff31a4afa9fb8612c7b"
                 ]
             ],
+            {
+                "versions_viralconsensus": [
+                    [
+                        "VIRALCONSENSUS",
+                        "viralconsensus",
+                        "viral_consensus v1.0.0"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-01-24T19:56:33.226459"
+    },
+    "sarscov2 - bam - with optional outputs": {
+        "content": [
             [
                 [
-                    "VIRALCONSENSUS",
-                    "viralconsensus",
-                    "viral_consensus v1.0.0"
+                    {
+                        "id": "test"
+                    },
+                    "test.consensus.fa:md5,8002717bf92a11fb4cf1bc97089063e3"
                 ]
-            ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.pos_counts.tsv:md5,94284ee424c75e13761452b4a18e4ad3"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.ins_counts.json:md5,b144d1a3bbb6c56dfc6376a198645d57"
+                ]
+            ],
+            {
+                "versions_viralconsensus": [
+                    [
+                        "VIRALCONSENSUS",
+                        "viralconsensus",
+                        "viral_consensus v1.0.0"
+                    ]
+                ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-14T15:23:36.859097"
+        "timestamp": "2026-01-24T19:56:42.830597"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/viralconsensus/tests/nextflow.config b/modules/nf-core/viralconsensus/tests/nextflow.config
index e221518b52da..50898f37a1cf 100644
--- a/modules/nf-core/viralconsensus/tests/nextflow.config
+++ b/modules/nf-core/viralconsensus/tests/nextflow.config
@@ -1,5 +1,5 @@
 process {
     withName: VIRALCONSENSUS {
-        ext.args = '-q 20 -d 10 -f 0.5'
+        ext.args = params.module_args
     }
 }
diff --git a/modules/nf-core/viralconsensus/tests/nextflow_optional.config b/modules/nf-core/viralconsensus/tests/nextflow_optional.config
deleted file mode 100644
index e221518b52da..000000000000
--- a/modules/nf-core/viralconsensus/tests/nextflow_optional.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: VIRALCONSENSUS {
-        ext.args = '-q 20 -d 10 -f 0.5'
-    }
-}