From 66588fcd100e084793b2d541194ece7fda32ff7c Mon Sep 17 00:00:00 2001
From: Maria Katsantoni <mariakatsantoni@Marias-MacBook-Air.local>
Date: Tue, 28 Oct 2025 16:19:48 +0100
Subject: [PATCH 01/12] fix: linting error

---
 .../nf-core/vembrane/table/environment.yml    |   7 +
 modules/nf-core/vembrane/table/main.nf        |  49 ++++
 modules/nf-core/vembrane/table/meta.yml       |  63 ++++
 .../nf-core/vembrane/table/tests/main.nf.test | 137 +++++++++
 .../vembrane/table/tests/main.nf.test.snap    | 270 ++++++++++++++++++
 .../vembrane/table/tests/nextflow.config      |   6 +
 6 files changed, 532 insertions(+)
 create mode 100644 modules/nf-core/vembrane/table/environment.yml
 create mode 100644 modules/nf-core/vembrane/table/main.nf
 create mode 100644 modules/nf-core/vembrane/table/meta.yml
 create mode 100644 modules/nf-core/vembrane/table/tests/main.nf.test
 create mode 100644 modules/nf-core/vembrane/table/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/vembrane/table/tests/nextflow.config

diff --git a/modules/nf-core/vembrane/table/environment.yml b/modules/nf-core/vembrane/table/environment.yml
new file mode 100644
index 00000000000..825a5fac4b7
--- /dev/null
+++ b/modules/nf-core/vembrane/table/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::vembrane=2.4.0
diff --git a/modules/nf-core/vembrane/table/main.nf b/modules/nf-core/vembrane/table/main.nf
new file mode 100644
index 00000000000..b7de2105c41
--- /dev/null
+++ b/modules/nf-core/vembrane/table/main.nf
@@ -0,0 +1,49 @@
+
+
+process VEMBRANE_TABLE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/vembrane:2.4.0--pyhdfd78af_0':
+        'biocontainers/vembrane:2.4.0--pyhdfd78af_0'}"
+
+    input:
+    tuple val(meta), path(vcf)
+    val expression
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: table
+    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}"
+    """
+    vembrane table \\
+        $args \\
+        --output ${prefix}.tsv \\
+        '$expression' \\
+        $vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vembrane: \$(vembrane --version 2>&1 | head -n1 | sed 's/vembrane //')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vembrane: \$(vembrane --version 2>&1 | head -n1 | sed 's/vembrane //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/vembrane/table/meta.yml b/modules/nf-core/vembrane/table/meta.yml
new file mode 100644
index 00000000000..2743421d4d6
--- /dev/null
+++ b/modules/nf-core/vembrane/table/meta.yml
@@ -0,0 +1,63 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "vembrane_table"
+description: Creates tabular (TSV) files from VCF/BCF data with flexible Python expressions
+keywords:
+  - vcf
+  - bcf
+  - table
+  - genomics
+  - variant
+  - annotation
+tools:
+  - "vembrane":
+      description: "Filter VCF/BCF files with Python expressions"
+      homepage: "https://vembrane.github.io/"
+      documentation: "https://github.com/vembrane/vembrane/blob/main/docs/table.md"
+      tool_dev_url: "https://github.com/vembrane/vembrane"
+      doi: "10.1093/bioinformatics/btac810"
+      licence: ["MIT"]
+      identifier: biotools:vembrane
+      args_id: "$args"
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - vcf:
+        type: file
+        description: VCF/BCF file to extract tabular data from
+        pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+        ontologies:
+          - edam: http://edamontology.org/format_3016 # VCF
+  - expression:
+      type: string
+      description: A comma-separated tuple of expressions that define the table column contents
+
+output:
+  table:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.tsv":
+          type: file
+          description: TSV file containing tabular data from VCF/BCF
+          pattern: "*.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+- "@mkatsanto"
+- "@trangdo-hsc"
+maintainers:
+- "@mkatsanto"
+- "@trangdo-hsc"
diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test b/modules/nf-core/vembrane/table/tests/main.nf.test
new file mode 100644
index 00000000000..8cb4ec33da0
--- /dev/null
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test
@@ -0,0 +1,137 @@
+
+nextflow_process {
+
+    name "Test Process VEMBRANE_TABLE"
+    script "../main.nf"
+    process "VEMBRANE_TABLE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vembrane"
+    tag "vembrane/table"
+
+    test("homo_sapiens - [vcf] - tsv") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true)
+                ]
+                input[1] = 'CHROM, POS, REF, ALT, QUAL'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [bcf.gz] - tsv") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bcf_gz'], checkIfExists: true)
+                ]
+                input[1] = 'CHROM, POS, REF, ALT, QUAL'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [vcf] - csv - custom_separator") {
+
+        config "./nextflow.config"
+
+        when {
+            params {
+                vembrane_args = '--separator ,'
+                vembrane_prefix = 'test.csv'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true)
+                ]
+                input[1] = 'CHROM, POS, REF, ALT'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [vcf] - tsv - custom_header") {
+
+        config "./nextflow.config"
+
+        when {
+            params {
+                vembrane_args = '--header "Chromosome,Position,Variant_ID,Quality"'
+                vembrane_prefix = 'test.custom_header'
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true)
+                ]
+                input[1] = 'CHROM, POS, ID, QUAL'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("homo_sapiens - [vcf] - tsv - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true)
+                ]
+                input[1] = 'CHROM, POS, REF, ALT, QUAL'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test.snap b/modules/nf-core/vembrane/table/tests/main.nf.test.snap
new file mode 100644
index 00000000000..f368bf75e9a
--- /dev/null
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test.snap
@@ -0,0 +1,270 @@
+{
+    "homo_sapiens - vcf": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,bc377c509db1bea19cb2d13b7e3b5480"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,bc377c509db1bea19cb2d13b7e3b5480"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T15:02:19.949621"
+    },
+    "homo_sapiens - [vcf] - tsv - custom_header": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.custom_header.tsv:md5,a000109bce654d2d6f8ce132c03d27b4"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.custom_header.tsv:md5,a000109bce654d2d6f8ce132c03d27b4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T16:01:22.053958"
+    },
+    "homo_sapiens - [vcf] - tsv": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,bc377c509db1bea19cb2d13b7e3b5480"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,bc377c509db1bea19cb2d13b7e3b5480"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T15:35:10.060963"
+    },
+    "sarscov2 - [bcf] - tsv": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "table": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T15:29:36.091335"
+    },
+    "homo_sapiens - [bcf.gz] - tsv": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,f0d357c993b9c0463b4564681ffffa2e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,f0d357c993b9c0463b4564681ffffa2e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T15:35:53.162346"
+    },
+    "homo_sapiens - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T15:02:57.900961"
+    },
+    "homo_sapiens - [vcf] - csv - custom_separator": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.csv.tsv:md5,f8616b2040be43518e270c02aac600f6"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.csv.tsv:md5,f8616b2040be43518e270c02aac600f6"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T15:45:34.223565"
+    },
+    "homo_sapiens - [vcf] - tsv - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ],
+                "table": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T15:24:08.270925"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/vembrane/table/tests/nextflow.config b/modules/nf-core/vembrane/table/tests/nextflow.config
new file mode 100644
index 00000000000..9c430bae52e
--- /dev/null
+++ b/modules/nf-core/vembrane/table/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: 'VEMBRANE_TABLE' {
+        ext.args = params.vembrane_args ?: ''
+        ext.prefix = { params.vembrane_prefix ?: "${meta.id}" }
+    }
+}

From fd659e31edd54d7cdfafc2b3bb5b629415572ab6 Mon Sep 17 00:00:00 2001
From: Maria Katsantoni <mariakatsantoni@Marias-MacBook-Air.local>
Date: Tue, 28 Oct 2025 17:07:34 +0100
Subject: [PATCH 02/12] fix: add conda snapshot

---
 .../vembrane/table/tests/main.nf.test.snap    | 93 -------------------
 1 file changed, 93 deletions(-)

diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test.snap b/modules/nf-core/vembrane/table/tests/main.nf.test.snap
index f368bf75e9a..26df26170bc 100644
--- a/modules/nf-core/vembrane/table/tests/main.nf.test.snap
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test.snap
@@ -1,39 +1,4 @@
 {
-    "homo_sapiens - vcf": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.tsv:md5,bc377c509db1bea19cb2d13b7e3b5480"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
-                ],
-                "table": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.tsv:md5,bc377c509db1bea19cb2d13b7e3b5480"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
-        },
-        "timestamp": "2025-10-28T15:02:19.949621"
-    },
     "homo_sapiens - [vcf] - tsv - custom_header": {
         "content": [
             {
@@ -104,29 +69,6 @@
         },
         "timestamp": "2025-10-28T15:35:10.060963"
     },
-    "sarscov2 - [bcf] - tsv": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "table": [
-                    
-                ],
-                "versions": [
-                    
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
-        },
-        "timestamp": "2025-10-28T15:29:36.091335"
-    },
     "homo_sapiens - [bcf.gz] - tsv": {
         "content": [
             {
@@ -162,41 +104,6 @@
         },
         "timestamp": "2025-10-28T15:35:53.162346"
     },
-    "homo_sapiens - vcf - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
-                ],
-                "table": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,24635137815ac702717f1edf14621d8c"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
-        },
-        "timestamp": "2025-10-28T15:02:57.900961"
-    },
     "homo_sapiens - [vcf] - csv - custom_separator": {
         "content": [
             {

From 28d37a0b6a231aa2bf3087d071baef7672250525 Mon Sep 17 00:00:00 2001
From: Maria Katsantoni <mariakatsantoni@Marias-MacBook-Air.local>
Date: Wed, 29 Oct 2025 09:55:24 +0100
Subject: [PATCH 03/12] fix: test path specification and removed test prefix

---
 modules/nf-core/vembrane/table/tests/main.nf.test    | 12 +++++-------
 .../nf-core/vembrane/table/tests/main.nf.test.snap   | 12 ++++++------
 modules/nf-core/vembrane/table/tests/nextflow.config |  1 -
 3 files changed, 11 insertions(+), 14 deletions(-)

diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test b/modules/nf-core/vembrane/table/tests/main.nf.test
index 8cb4ec33da0..6ada32e843d 100644
--- a/modules/nf-core/vembrane/table/tests/main.nf.test
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, REF, ALT, QUAL'
                 """
@@ -39,7 +39,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['popgen']['plink_case_control_bcf_gz'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bcf.gz', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, REF, ALT, QUAL'
                 """
@@ -61,13 +61,12 @@ nextflow_process {
         when {
             params {
                 vembrane_args = '--separator ,'
-                vembrane_prefix = 'test.csv'
             }
             process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, REF, ALT'
                 """
@@ -89,13 +88,12 @@ nextflow_process {
         when {
             params {
                 vembrane_args = '--header "Chromosome,Position,Variant_ID,Quality"'
-                vembrane_prefix = 'test.custom_header'
             }
             process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, ID, QUAL'
                 """
@@ -119,7 +117,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, REF, ALT, QUAL'
                 """
diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test.snap b/modules/nf-core/vembrane/table/tests/main.nf.test.snap
index 26df26170bc..75d5ed95413 100644
--- a/modules/nf-core/vembrane/table/tests/main.nf.test.snap
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.custom_header.tsv:md5,a000109bce654d2d6f8ce132c03d27b4"
+                        "test.tsv:md5,a000109bce654d2d6f8ce132c03d27b4"
                     ]
                 ],
                 "1": [
@@ -20,7 +20,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.custom_header.tsv:md5,a000109bce654d2d6f8ce132c03d27b4"
+                        "test.tsv:md5,a000109bce654d2d6f8ce132c03d27b4"
                     ]
                 ],
                 "versions": [
@@ -32,7 +32,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T16:01:22.053958"
+        "timestamp": "2025-10-29T09:52:24.816246"
     },
     "homo_sapiens - [vcf] - tsv": {
         "content": [
@@ -113,7 +113,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.csv.tsv:md5,f8616b2040be43518e270c02aac600f6"
+                        "test.tsv:md5,f8616b2040be43518e270c02aac600f6"
                     ]
                 ],
                 "1": [
@@ -125,7 +125,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.csv.tsv:md5,f8616b2040be43518e270c02aac600f6"
+                        "test.tsv:md5,f8616b2040be43518e270c02aac600f6"
                     ]
                 ],
                 "versions": [
@@ -137,7 +137,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:45:34.223565"
+        "timestamp": "2025-10-29T09:53:37.401847"
     },
     "homo_sapiens - [vcf] - tsv - stub": {
         "content": [
diff --git a/modules/nf-core/vembrane/table/tests/nextflow.config b/modules/nf-core/vembrane/table/tests/nextflow.config
index 9c430bae52e..95dbb06496f 100644
--- a/modules/nf-core/vembrane/table/tests/nextflow.config
+++ b/modules/nf-core/vembrane/table/tests/nextflow.config
@@ -1,6 +1,5 @@
 process {
     withName: 'VEMBRANE_TABLE' {
         ext.args = params.vembrane_args ?: ''
-        ext.prefix = { params.vembrane_prefix ?: "${meta.id}" }
     }
 }

From 3dfa74b80d242fa1629140a2e4b15898f8d6bf23 Mon Sep 17 00:00:00 2001
From: Maria Katsantoni <mariakatsantoni@Marias-MacBook-Air.local>
Date: Wed, 29 Oct 2025 14:27:12 +0100
Subject: [PATCH 04/12] fix: add explicit version displayed

---
 .../nf-core/vembrane/table/tests/main.nf.test | 25 +++++++++++++++----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test b/modules/nf-core/vembrane/table/tests/main.nf.test
index 6ada32e843d..b899e6ef291 100644
--- a/modules/nf-core/vembrane/table/tests/main.nf.test
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test
@@ -27,7 +27,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
     }
@@ -49,7 +52,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
     }
@@ -76,7 +82,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
     }
@@ -103,7 +112,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
     }
@@ -127,7 +139,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
     }

From 1e91998df1e02afcc3e0bcb342494afdb3261cd6 Mon Sep 17 00:00:00 2001
From: Maria Katsantoni <mariakatsantoni@Marias-MacBook-Air.local>
Date: Wed, 29 Oct 2025 14:51:19 +0100
Subject: [PATCH 05/12] fix: revert the snapshot syntax

---
 .../nf-core/vembrane/table/tests/main.nf.test | 25 ++++---------------
 1 file changed, 5 insertions(+), 20 deletions(-)

diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test b/modules/nf-core/vembrane/table/tests/main.nf.test
index b899e6ef291..6ada32e843d 100644
--- a/modules/nf-core/vembrane/table/tests/main.nf.test
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test
@@ -27,10 +27,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -52,10 +49,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -82,10 +76,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -112,10 +103,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -139,10 +127,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).yaml
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
     }

From e268108f65a7474cb0f9a0ec67f247999f241034 Mon Sep 17 00:00:00 2001
From: Maria Katsantoni <mariakatsantoni@Marias-MacBook-Air.local>
Date: Wed, 29 Oct 2025 15:16:55 +0100
Subject: [PATCH 06/12] fix: explicit version snapshot retry

---
 modules/nf-core/vembrane/table/tests/main.nf.test      | 5 ++++-
 modules/nf-core/vembrane/table/tests/main.nf.test.snap | 7 ++++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test b/modules/nf-core/vembrane/table/tests/main.nf.test
index 6ada32e843d..05a0acb1f22 100644
--- a/modules/nf-core/vembrane/table/tests/main.nf.test
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test
@@ -127,7 +127,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
     }
diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test.snap b/modules/nf-core/vembrane/table/tests/main.nf.test.snap
index 75d5ed95413..82b9eb3bf88 100644
--- a/modules/nf-core/vembrane/table/tests/main.nf.test.snap
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test.snap
@@ -166,12 +166,17 @@
                 "versions": [
                     "versions.yml:md5,24635137815ac702717f1edf14621d8c"
                 ]
+            },
+            {
+                "VEMBRANE_TABLE": {
+                    "vembrane": "2.4.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:24:08.270925"
+        "timestamp": "2025-10-29T15:05:52.03881"
     }
 }
\ No newline at end of file

From 2dae3921efddc0c7d5a067ba2ad4f2a1c2563ef9 Mon Sep 17 00:00:00 2001
From: Maria Katsantoni <mariakatsantoni@Marias-MacBook-Air.local>
Date: Wed, 29 Oct 2025 15:41:28 +0100
Subject: [PATCH 07/12] fix: remove newline

---
 modules/nf-core/vembrane/table/main.nf | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/modules/nf-core/vembrane/table/main.nf b/modules/nf-core/vembrane/table/main.nf
index b7de2105c41..4ea16c29667 100644
--- a/modules/nf-core/vembrane/table/main.nf
+++ b/modules/nf-core/vembrane/table/main.nf
@@ -1,13 +1,11 @@
-
-
 process VEMBRANE_TABLE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/vembrane:2.4.0--pyhdfd78af_0':
-        'biocontainers/vembrane:2.4.0--pyhdfd78af_0'}"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/vembrane:2.4.0--pyhdfd78af_0'
+        : 'biocontainers/vembrane:2.4.0--pyhdfd78af_0'}"
 
     input:
     tuple val(meta), path(vcf)
@@ -15,7 +13,7 @@ process VEMBRANE_TABLE {
 
     output:
     tuple val(meta), path("*.tsv"), emit: table
-    path "versions.yml"           , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,10 +23,10 @@ process VEMBRANE_TABLE {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     vembrane table \\
-        $args \\
+        ${args} \\
         --output ${prefix}.tsv \\
-        '$expression' \\
-        $vcf
+        '${expression}' \\
+        ${vcf}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From d707a842c25db0d0818b117cfe3e4ce37c02478b Mon Sep 17 00:00:00 2001
From: Maria Katsantoni <31883096+mkatsanto@users.noreply.github.com>
Date: Wed, 29 Oct 2025 16:09:01 +0100
Subject: [PATCH 08/12] Update
 modules/nf-core/vembrane/table/tests/main.nf.test
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
---
 modules/nf-core/vembrane/table/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test b/modules/nf-core/vembrane/table/tests/main.nf.test
index 05a0acb1f22..a69bf39573b 100644
--- a/modules/nf-core/vembrane/table/tests/main.nf.test
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, REF, ALT, QUAL'

From 33daff0e72cce2d2d2bb0bf6d3775073620d913c Mon Sep 17 00:00:00 2001
From: Maria Katsantoni <31883096+mkatsanto@users.noreply.github.com>
Date: Wed, 29 Oct 2025 16:10:10 +0100
Subject: [PATCH 09/12] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
---
 modules/nf-core/vembrane/table/tests/main.nf.test | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test b/modules/nf-core/vembrane/table/tests/main.nf.test
index a69bf39573b..bfc7595e77b 100644
--- a/modules/nf-core/vembrane/table/tests/main.nf.test
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test
@@ -1,4 +1,3 @@
-
 nextflow_process {
 
     name "Test Process VEMBRANE_TABLE"
@@ -38,7 +37,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bcf.gz', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, REF, ALT, QUAL'
@@ -65,7 +64,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, REF, ALT'
@@ -92,7 +91,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, ID, QUAL'
@@ -116,7 +115,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, REF, ALT, QUAL'

From afcbc53ab8fc129ce7478bdfa3829b3bd8428386 Mon Sep 17 00:00:00 2001
From: Maria Katsantoni <mariakatsantoni@Marias-MacBook-Air.local>
Date: Wed, 29 Oct 2025 16:52:46 +0100
Subject: [PATCH 10/12] fix: apply formatting code review changes

---
 .../nf-core/vembrane/table/tests/main.nf.test | 11 +++--
 .../vembrane/table/tests/main.nf.test.snap    | 40 +++++++------------
 .../vembrane/table/tests/nextflow.config      |  2 +-
 3 files changed, 21 insertions(+), 32 deletions(-)

diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test b/modules/nf-core/vembrane/table/tests/main.nf.test
index 05a0acb1f22..bfc7595e77b 100644
--- a/modules/nf-core/vembrane/table/tests/main.nf.test
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test
@@ -1,4 +1,3 @@
-
 nextflow_process {
 
     name "Test Process VEMBRANE_TABLE"
@@ -16,7 +15,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, REF, ALT, QUAL'
@@ -38,7 +37,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bcf.gz', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, REF, ALT, QUAL'
@@ -65,7 +64,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, REF, ALT'
@@ -92,7 +91,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, ID, QUAL'
@@ -116,7 +115,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true)
                 ]
                 input[1] = 'CHROM, POS, REF, ALT, QUAL'
diff --git a/modules/nf-core/vembrane/table/tests/main.nf.test.snap b/modules/nf-core/vembrane/table/tests/main.nf.test.snap
index 82b9eb3bf88..afc04910885 100644
--- a/modules/nf-core/vembrane/table/tests/main.nf.test.snap
+++ b/modules/nf-core/vembrane/table/tests/main.nf.test.snap
@@ -5,8 +5,7 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.tsv:md5,a000109bce654d2d6f8ce132c03d27b4"
                     ]
@@ -17,8 +16,7 @@
                 "table": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.tsv:md5,a000109bce654d2d6f8ce132c03d27b4"
                     ]
@@ -32,7 +30,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T09:52:24.816246"
+        "timestamp": "2025-10-29T16:45:22.931526"
     },
     "homo_sapiens - [vcf] - tsv": {
         "content": [
@@ -40,8 +38,7 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.tsv:md5,bc377c509db1bea19cb2d13b7e3b5480"
                     ]
@@ -52,8 +49,7 @@
                 "table": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.tsv:md5,bc377c509db1bea19cb2d13b7e3b5480"
                     ]
@@ -67,7 +63,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:35:10.060963"
+        "timestamp": "2025-10-29T16:44:33.392488"
     },
     "homo_sapiens - [bcf.gz] - tsv": {
         "content": [
@@ -75,8 +71,7 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.tsv:md5,f0d357c993b9c0463b4564681ffffa2e"
                     ]
@@ -87,8 +82,7 @@
                 "table": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.tsv:md5,f0d357c993b9c0463b4564681ffffa2e"
                     ]
@@ -102,7 +96,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-28T15:35:53.162346"
+        "timestamp": "2025-10-29T16:44:48.817287"
     },
     "homo_sapiens - [vcf] - csv - custom_separator": {
         "content": [
@@ -110,8 +104,7 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.tsv:md5,f8616b2040be43518e270c02aac600f6"
                     ]
@@ -122,8 +115,7 @@
                 "table": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.tsv:md5,f8616b2040be43518e270c02aac600f6"
                     ]
@@ -137,7 +129,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T09:53:37.401847"
+        "timestamp": "2025-10-29T16:45:03.973682"
     },
     "homo_sapiens - [vcf] - tsv - stub": {
         "content": [
@@ -145,8 +137,7 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -157,8 +148,7 @@
                 "table": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -177,6 +167,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.0"
         },
-        "timestamp": "2025-10-29T15:05:52.03881"
+        "timestamp": "2025-10-29T16:45:36.132566"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/vembrane/table/tests/nextflow.config b/modules/nf-core/vembrane/table/tests/nextflow.config
index 95dbb06496f..77acb7b7741 100644
--- a/modules/nf-core/vembrane/table/tests/nextflow.config
+++ b/modules/nf-core/vembrane/table/tests/nextflow.config
@@ -2,4 +2,4 @@ process {
     withName: 'VEMBRANE_TABLE' {
         ext.args = params.vembrane_args ?: ''
     }
-}
+}
\ No newline at end of file

From 0589efd4577854d66b0e58e2ec4b494388a063e7 Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Sat, 1 Nov 2025 12:13:53 +0000
Subject: [PATCH 11/12] Update modules/nf-core/vembrane/table/main.nf

---
 modules/nf-core/vembrane/table/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/vembrane/table/main.nf b/modules/nf-core/vembrane/table/main.nf
index 4ea16c29667..96eaf89bf52 100644
--- a/modules/nf-core/vembrane/table/main.nf
+++ b/modules/nf-core/vembrane/table/main.nf
@@ -30,7 +30,7 @@ process VEMBRANE_TABLE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vembrane: \$(vembrane --version 2>&1 | head -n1 | sed 's/vembrane //')
+        vembrane: \$(vembrane --version | sed '1!d;s/.* //')
     END_VERSIONS
     """
 

From 06fe195a60dd81c95f481afebe9baece007360ec Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Sat, 1 Nov 2025 13:02:33 +0000
Subject: [PATCH 12/12] Update modules/nf-core/vembrane/table/main.nf

---
 modules/nf-core/vembrane/table/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/vembrane/table/main.nf b/modules/nf-core/vembrane/table/main.nf
index 96eaf89bf52..243ce472b36 100644
--- a/modules/nf-core/vembrane/table/main.nf
+++ b/modules/nf-core/vembrane/table/main.nf
@@ -41,7 +41,7 @@ process VEMBRANE_TABLE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vembrane: \$(vembrane --version 2>&1 | head -n1 | sed 's/vembrane //')
+        vembrane: \$(vembrane --version | sed '1!d;s/.* //')
     END_VERSIONS
     """
 }