From 6cf01ef069fcf0203a7b9a27c031836a66ebda71 Mon Sep 17 00:00:00 2001
From: trangdo <trang.do@holzerscientific.com>
Date: Tue, 28 Oct 2025 16:41:17 +0100
Subject: [PATCH 1/8] Hackathon - Add vembrane filter module

---
 .../nf-core/vembrane/filter/environment.yml   |  10 ++
 modules/nf-core/vembrane/filter/main.nf       |  75 ++++++++++++
 modules/nf-core/vembrane/filter/meta.yml      |  62 ++++++++++
 .../vembrane/filter/tests/main.nf.test        | 110 ++++++++++++++++++
 4 files changed, 257 insertions(+)
 create mode 100644 modules/nf-core/vembrane/filter/environment.yml
 create mode 100644 modules/nf-core/vembrane/filter/main.nf
 create mode 100644 modules/nf-core/vembrane/filter/meta.yml
 create mode 100644 modules/nf-core/vembrane/filter/tests/main.nf.test

diff --git a/modules/nf-core/vembrane/filter/environment.yml b/modules/nf-core/vembrane/filter/environment.yml
new file mode 100644
index 000000000000..a33c9cdff966
--- /dev/null
+++ b/modules/nf-core/vembrane/filter/environment.yml
@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  # TODO nf-core: List required Conda package(s).
+  #               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+  #               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+  - "bioconda::vembrane=2.4.0"
diff --git a/modules/nf-core/vembrane/filter/main.nf b/modules/nf-core/vembrane/filter/main.nf
new file mode 100644
index 000000000000..70f06410f890
--- /dev/null
+++ b/modules/nf-core/vembrane/filter/main.nf
@@ -0,0 +1,75 @@
+// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
+//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided using the "task.ext" directive, see here:
+//               https://www.nextflow.io/docs/latest/process.html#ext
+//               where "task.ext" is a string.
+//               Any parameters that need to be evaluated in the context of a particular sample
+//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
+// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
+//               unless there is a run-time, storage advantage in implementing in this way
+//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
+//                 bwa mem | samtools view -B -T ref.fasta
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
+//               list (`[]`) instead of a file can be used to work around this issue.
+
+process VEMBRANE_FILTER {
+    tag "$meta.id"
+    label 'process_single'
+
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
+        'biocontainers/vembrane:2.4.0--pyhdfd78af_0' }"
+    // container "quay.io/biocontainers/vembrane:2.4.0--pyhdfd78af_0"
+
+    input:
+    tuple val(meta), path(variant)
+    val(expression)
+
+    output:
+    tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: filtered_variant
+    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 filter \\
+        ${args} \\
+        ${expression} \\
+        -o ${prefix}_filtered.vcf \\
+        $variant
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vembrane: \$(vembrane --version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo $args
+
+    vembrane filter \\
+        ${args} \\
+        ${expression} \\
+        -o ${prefix}_filtered.vcf \\
+        $variant
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vembrane: \$(vembrane --version)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/vembrane/filter/meta.yml b/modules/nf-core/vembrane/filter/meta.yml
new file mode 100644
index 000000000000..ab25455c3724
--- /dev/null
+++ b/modules/nf-core/vembrane/filter/meta.yml
@@ -0,0 +1,62 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+# # TODO nf-core: Add a description of the module and list keywords
+name: "vembrane_filter"
+description: write your description here
+keywords:
+  - filter
+  - table
+  - sort
+tools:
+  ## TODO nf-core: Add a description and other details for the software below
+  - "vembrane":
+      description: "Filter VCF/BCF files with Python expressions."
+      homepage: "https://github.com/vembrane/vembrane/tree/main"
+      documentation: "https://github.com/vembrane/vembrane/blob/main/docs/filter.md"
+      tool_dev_url: "https://github.com/vembrane/vembrane.git"
+      doi: "10.1093/bioinformatics/btac810"
+      licence: ["MIT"]
+      identifier: biotools:vembrane/filter
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - variant:
+        type: file
+        description: |
+          Path to the VCF/BCF file to be filtered.
+          e.g. 'file.vcf', 'file.vcf.gz', 'file.bcf', 'file.bcf.gz'
+        ontologies: []
+  - expression:
+      type: string
+      description: |
+        The filter expression can be any valid python expression that evaluates to a value of type bool.
+        e.g. 'ANN["SYMBOL"] == "CDH2"'
+      ontologies: []
+
+output:
+  filtered_variant:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.{vcf,bcf,vcf.gz,bcf.gz}":
+          type: file
+          description: VCF normalized output file
+          pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@trangdo-hsc"
+  - "@mkatsanto"
+maintainers:
+  - "@trangdo-hsc"
diff --git a/modules/nf-core/vembrane/filter/tests/main.nf.test b/modules/nf-core/vembrane/filter/tests/main.nf.test
new file mode 100644
index 000000000000..c08e6cc4e862
--- /dev/null
+++ b/modules/nf-core/vembrane/filter/tests/main.nf.test
@@ -0,0 +1,110 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test vembrane
+nextflow_process {
+
+    name "Test Process VEMBRANE"
+    script "../main.nf"
+    process "VEMBRANE_FILTER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vembrane"
+    tag "vembrane/filter"
+
+    test("homo sapiens - vcf") {
+
+        //
+        // (the module requires running more than one process to generate the required output)
+        // add the 'setup' method here.
+        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true),
+                ]
+                input[1] = "'QUAL >= 30'"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.filtered_variant).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - vcf.gz") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true),
+                ]
+                input[1] = "'QUAL >= 30'"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.filtered_variant
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - bcf") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.bcf', checkIfExists: true),
+                ]
+                input[1] = "'QUAL >= 30'"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.filtered_variant).match() }
+            )
+        }
+
+    }
+
+test("homo sapiens - bcf.gz") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bcf.gz', checkIfExists: true),
+                ]
+                input[1] = "'QUAL >= 30'"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.filtered_variant).match() }
+            )
+        }
+
+    }
+
+}

From 0155088ed26273f5163744e76432cff8813f5aef Mon Sep 17 00:00:00 2001
From: trangdo <trang.do@holzerscientific.com>
Date: Tue, 28 Oct 2025 16:51:29 +0100
Subject: [PATCH 2/8] Prepare for merge

---
 modules/nf-core/vembrane/filter/main.nf       | 19 -----
 modules/nf-core/vembrane/filter/meta.yml      |  2 -
 .../vembrane/filter/tests/main.nf.test        |  2 -
 .../vembrane/filter/tests/main.nf.test.snap   | 74 +++++++++++++++++++
 4 files changed, 74 insertions(+), 23 deletions(-)
 create mode 100644 modules/nf-core/vembrane/filter/tests/main.nf.test.snap

diff --git a/modules/nf-core/vembrane/filter/main.nf b/modules/nf-core/vembrane/filter/main.nf
index 70f06410f890..30c283667ed2 100644
--- a/modules/nf-core/vembrane/filter/main.nf
+++ b/modules/nf-core/vembrane/filter/main.nf
@@ -1,30 +1,11 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process VEMBRANE_FILTER {
     tag "$meta.id"
     label 'process_single'
 
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
         'biocontainers/vembrane:2.4.0--pyhdfd78af_0' }"
-    // container "quay.io/biocontainers/vembrane:2.4.0--pyhdfd78af_0"
 
     input:
     tuple val(meta), path(variant)
diff --git a/modules/nf-core/vembrane/filter/meta.yml b/modules/nf-core/vembrane/filter/meta.yml
index ab25455c3724..f88c73913918 100644
--- a/modules/nf-core/vembrane/filter/meta.yml
+++ b/modules/nf-core/vembrane/filter/meta.yml
@@ -1,5 +1,4 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-# # TODO nf-core: Add a description of the module and list keywords
 name: "vembrane_filter"
 description: write your description here
 keywords:
@@ -7,7 +6,6 @@ keywords:
   - table
   - sort
 tools:
-  ## TODO nf-core: Add a description and other details for the software below
   - "vembrane":
       description: "Filter VCF/BCF files with Python expressions."
       homepage: "https://github.com/vembrane/vembrane/tree/main"
diff --git a/modules/nf-core/vembrane/filter/tests/main.nf.test b/modules/nf-core/vembrane/filter/tests/main.nf.test
index c08e6cc4e862..ada63541adee 100644
--- a/modules/nf-core/vembrane/filter/tests/main.nf.test
+++ b/modules/nf-core/vembrane/filter/tests/main.nf.test
@@ -1,5 +1,3 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core modules test vembrane
 nextflow_process {
 
     name "Test Process VEMBRANE"
diff --git a/modules/nf-core/vembrane/filter/tests/main.nf.test.snap b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
new file mode 100644
index 000000000000..17ed0c4d251d
--- /dev/null
+++ b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
@@ -0,0 +1,74 @@
+{
+    "homo sapiens - bcf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_filtered.vcf:md5,38f3479f9071fbe018226be0aac62354"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-10-28T16:35:15.82704"
+    },
+    "homo sapiens - vcf.gz": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_filtered.vcf:md5,44659c255c5018ba2e5a3b4b80797a57"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-10-28T16:35:10.958678"
+    },
+    "homo sapiens - bcf.gz": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_filtered.vcf:md5,c9be02b5c5e036c25e05f59a94528203"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-10-28T16:35:21.012789"
+    },
+    "homo sapiens - vcf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_filtered.vcf:md5,20af56305296f2b0e52979465f19804b"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-10-28T16:35:06.185151"
+    }
+}
\ No newline at end of file

From 0a600e7f6fa81a3d816c04fe6fd586fa21ee65d9 Mon Sep 17 00:00:00 2001
From: trangdo <trang.do@holzerscientific.com>
Date: Tue, 28 Oct 2025 17:10:32 +0100
Subject: [PATCH 3/8] Prepare for merge

---
 .../nf-core/vembrane/filter/environment.yml   |   3 -
 modules/nf-core/vembrane/filter/main.nf       |   2 +-
 .../vembrane/filter/tests/main.nf.test        |   8 +-
 .../vembrane/filter/tests/main.nf.test.snap   | 140 +++++++++++++-----
 4 files changed, 109 insertions(+), 44 deletions(-)

diff --git a/modules/nf-core/vembrane/filter/environment.yml b/modules/nf-core/vembrane/filter/environment.yml
index a33c9cdff966..fc61617b4e79 100644
--- a/modules/nf-core/vembrane/filter/environment.yml
+++ b/modules/nf-core/vembrane/filter/environment.yml
@@ -4,7 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  # TODO nf-core: List required Conda package(s).
-  #               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-  #               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
   - "bioconda::vembrane=2.4.0"
diff --git a/modules/nf-core/vembrane/filter/main.nf b/modules/nf-core/vembrane/filter/main.nf
index 30c283667ed2..5e56de3830e0 100644
--- a/modules/nf-core/vembrane/filter/main.nf
+++ b/modules/nf-core/vembrane/filter/main.nf
@@ -4,7 +4,7 @@ process VEMBRANE_FILTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
+        'https://depot.galaxyproject.org/singularity/vembrane:2.4.0--pyhdfd78af_0':
         'biocontainers/vembrane:2.4.0--pyhdfd78af_0' }"
 
     input:
diff --git a/modules/nf-core/vembrane/filter/tests/main.nf.test b/modules/nf-core/vembrane/filter/tests/main.nf.test
index ada63541adee..4a3e2f364255 100644
--- a/modules/nf-core/vembrane/filter/tests/main.nf.test
+++ b/modules/nf-core/vembrane/filter/tests/main.nf.test
@@ -31,7 +31,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.filtered_variant).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -54,7 +54,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.filtered_variant
+                    process.out
                     ).match() }
             )
         }
@@ -77,7 +77,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.filtered_variant).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
@@ -99,7 +99,7 @@ test("homo sapiens - bcf.gz") {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.filtered_variant).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/vembrane/filter/tests/main.nf.test.snap b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
index 17ed0c4d251d..0bc3b16cf7e5 100644
--- a/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
+++ b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
@@ -1,74 +1,142 @@
 {
     "homo sapiens - bcf": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_filtered.vcf:md5,38f3479f9071fbe018226be0aac62354"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_filtered.vcf:md5,38f3479f9071fbe018226be0aac62354"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
+                ],
+                "filtered_variant": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_filtered.vcf:md5,38f3479f9071fbe018226be0aac62354"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-28T16:35:15.82704"
+        "timestamp": "2025-10-29T10:40:44.493576"
     },
     "homo sapiens - vcf.gz": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_filtered.vcf:md5,44659c255c5018ba2e5a3b4b80797a57"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_filtered.vcf:md5,44659c255c5018ba2e5a3b4b80797a57"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
+                ],
+                "filtered_variant": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_filtered.vcf:md5,44659c255c5018ba2e5a3b4b80797a57"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-28T16:35:10.958678"
+        "timestamp": "2025-10-29T10:40:40.227725"
     },
     "homo sapiens - bcf.gz": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_filtered.vcf:md5,c9be02b5c5e036c25e05f59a94528203"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_filtered.vcf:md5,c9be02b5c5e036c25e05f59a94528203"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
+                ],
+                "filtered_variant": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_filtered.vcf:md5,c9be02b5c5e036c25e05f59a94528203"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-28T16:35:21.012789"
+        "timestamp": "2025-10-29T10:40:49.157452"
     },
     "homo sapiens - vcf": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_filtered.vcf:md5,20af56305296f2b0e52979465f19804b"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_filtered.vcf:md5,20af56305296f2b0e52979465f19804b"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
+                ],
+                "filtered_variant": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_filtered.vcf:md5,20af56305296f2b0e52979465f19804b"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
                 ]
-            ]
+            }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-28T16:35:06.185151"
+        "timestamp": "2025-10-29T10:40:35.909472"
     }
 }
\ No newline at end of file

From 5d1333fb23d47cea83d36a11f1c149d8fda91f64 Mon Sep 17 00:00:00 2001
From: dhtt <dhthutrang@gmail.com>
Date: Wed, 5 Nov 2025 11:44:55 +0100
Subject: [PATCH 4/8] Format, updates yml, add stub tests to vembrane/filter

---
 modules/nf-core/vembrane/filter/main.nf       |  19 +-
 modules/nf-core/vembrane/filter/meta.yml      |  13 +-
 .../vembrane/filter/tests/main.nf.test        | 114 +++++++++-
 .../vembrane/filter/tests/main.nf.test.snap   | 196 ++++++++++++++----
 4 files changed, 279 insertions(+), 63 deletions(-)

diff --git a/modules/nf-core/vembrane/filter/main.nf b/modules/nf-core/vembrane/filter/main.nf
index 5e56de3830e0..57d3869cc166 100644
--- a/modules/nf-core/vembrane/filter/main.nf
+++ b/modules/nf-core/vembrane/filter/main.nf
@@ -13,7 +13,7 @@ process VEMBRANE_FILTER {
 
     output:
     tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: filtered_variant
-    path "versions.yml"           , emit: versions
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,31 +26,24 @@ process VEMBRANE_FILTER {
     vembrane filter \\
         ${args} \\
         ${expression} \\
-        -o ${prefix}_filtered.vcf \\
-        $variant
+        -o ${prefix}.filtered.vcf \\
+        ${variant}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vembrane: \$(vembrane --version)
+        vembrane: \$(vembrane --version | sed '1!d;s/.* //')
     END_VERSIONS
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    echo $args
-
-    vembrane filter \\
-        ${args} \\
-        ${expression} \\
-        -o ${prefix}_filtered.vcf \\
-        $variant
+    touch ${prefix}.filtered.vcf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        vembrane: \$(vembrane --version)
+        vembrane: \$(vembrane --version | sed '1!d;s/.* //')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/vembrane/filter/meta.yml b/modules/nf-core/vembrane/filter/meta.yml
index f88c73913918..2d6767be23cc 100644
--- a/modules/nf-core/vembrane/filter/meta.yml
+++ b/modules/nf-core/vembrane/filter/meta.yml
@@ -3,8 +3,11 @@ name: "vembrane_filter"
 description: write your description here
 keywords:
   - filter
-  - table
-  - sort
+  - vcf
+  - bcf
+  - genomics
+  - variant
+  - annotation
 tools:
   - "vembrane":
       description: "Filter VCF/BCF files with Python expressions."
@@ -20,7 +23,7 @@ input:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test' ]
     - variant:
         type: file
         description: |
@@ -40,10 +43,10 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*.{vcf,bcf,vcf.gz,bcf.gz}":
           type: file
-          description: VCF normalized output file
+          description: Filtered VCF output file
           pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
           ontologies: []
   versions:
diff --git a/modules/nf-core/vembrane/filter/tests/main.nf.test b/modules/nf-core/vembrane/filter/tests/main.nf.test
index 4a3e2f364255..dff81dc5ea00 100644
--- a/modules/nf-core/vembrane/filter/tests/main.nf.test
+++ b/modules/nf-core/vembrane/filter/tests/main.nf.test
@@ -11,16 +11,11 @@ nextflow_process {
 
     test("homo sapiens - vcf") {
 
-        //
-        // (the module requires running more than one process to generate the required output)
-        // add the 'setup' method here.
-        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
-
         when {
             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] = "'QUAL >= 30'"
@@ -42,7 +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.vcf.gz', checkIfExists: true),
                 ]
                 input[1] = "'QUAL >= 30'"
@@ -66,7 +61,7 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
+                    [ id:'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.bcf', checkIfExists: true),
                 ]
                 input[1] = "'QUAL >= 30'"
@@ -88,7 +83,7 @@ test("homo sapiens - bcf.gz") {
             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] = "'QUAL >= 30'"
@@ -105,4 +100,105 @@ test("homo sapiens - bcf.gz") {
 
     }
 
+    test("homo sapiens - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf', checkIfExists: true),
+                ]
+                input[1] = "'QUAL >= 30'"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - vcf.gz - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.vcf.gz', checkIfExists: true),
+                ]
+                input[1] = "'QUAL >= 30'"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("homo sapiens - bcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.bcf', checkIfExists: true),
+                ]
+                input[1] = "'QUAL >= 30'"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+test("homo sapiens - bcf.gz - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.bcf.gz', checkIfExists: true),
+                ]
+                input[1] = "'QUAL >= 30'"
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
 }
diff --git a/modules/nf-core/vembrane/filter/tests/main.nf.test.snap b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
index 0bc3b16cf7e5..a00a8f3c32fb 100644
--- a/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
+++ b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
@@ -5,26 +5,24 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test_filtered.vcf:md5,38f3479f9071fbe018226be0aac62354"
+                        "test.filtered.vcf:md5,6c1393e34fc3ffe763b7c75725176463"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ],
                 "filtered_variant": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test_filtered.vcf:md5,38f3479f9071fbe018226be0aac62354"
+                        "test.filtered.vcf:md5,6c1393e34fc3ffe763b7c75725176463"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
             }
         ],
@@ -32,7 +30,40 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-29T10:40:44.493576"
+        "timestamp": "2025-11-05T11:14:07.57913"
+    },
+    "homo sapiens - bcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
+                ],
+                "filtered_variant": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-11-05T11:14:22.290473"
     },
     "homo sapiens - vcf.gz": {
         "content": [
@@ -40,26 +71,57 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
+                        },
+                        "test.filtered.vcf:md5,75cc37af6bc118370251fee6ab1532ee"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
+                ],
+                "filtered_variant": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.vcf:md5,75cc37af6bc118370251fee6ab1532ee"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-11-05T11:14:03.41245"
+    },
+    "homo sapiens - vcf.gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
                         },
-                        "test_filtered.vcf:md5,44659c255c5018ba2e5a3b4b80797a57"
+                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ],
                 "filtered_variant": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test_filtered.vcf:md5,44659c255c5018ba2e5a3b4b80797a57"
+                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
             }
         ],
@@ -67,7 +129,40 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-29T10:40:40.227725"
+        "timestamp": "2025-11-05T11:14:18.955755"
+    },
+    "homo sapiens - bcf.gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
+                ],
+                "filtered_variant": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-11-05T11:14:26.669552"
     },
     "homo sapiens - bcf.gz": {
         "content": [
@@ -75,26 +170,24 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test_filtered.vcf:md5,c9be02b5c5e036c25e05f59a94528203"
+                        "test.filtered.vcf:md5,71c159f1c953e33c94ad6fd5efbf719b"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ],
                 "filtered_variant": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test_filtered.vcf:md5,c9be02b5c5e036c25e05f59a94528203"
+                        "test.filtered.vcf:md5,71c159f1c953e33c94ad6fd5efbf719b"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
             }
         ],
@@ -102,7 +195,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-29T10:40:49.157452"
+        "timestamp": "2025-11-05T11:14:12.225232"
     },
     "homo sapiens - vcf": {
         "content": [
@@ -110,26 +203,57 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
+                        },
+                        "test.filtered.vcf:md5,116c742876dd0ab00a936178f1da9c86"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
+                ],
+                "filtered_variant": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.filtered.vcf:md5,116c742876dd0ab00a936178f1da9c86"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-11-05T11:13:59.313832"
+    },
+    "homo sapiens - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
                         },
-                        "test_filtered.vcf:md5,20af56305296f2b0e52979465f19804b"
+                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ],
                 "filtered_variant": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test_filtered.vcf:md5,20af56305296f2b0e52979465f19804b"
+                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,78268fef6c3acebb6a431844197f42d5"
+                    "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
             }
         ],
@@ -137,6 +261,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-10-29T10:40:35.909472"
+        "timestamp": "2025-11-05T11:14:15.550717"
     }
 }
\ No newline at end of file

From f93e871edd8b9074f70b81b5f2a3fd5a7592374b Mon Sep 17 00:00:00 2001
From: trangdo <trang.do@holzerscientific.com>
Date: Tue, 28 Oct 2025 16:51:29 +0100
Subject: [PATCH 5/8] Prepare for merge

---
 .../vembrane/filter/tests/main.nf.test.snap   | 64 +++++++++++++++++++
 1 file changed, 64 insertions(+)

diff --git a/modules/nf-core/vembrane/filter/tests/main.nf.test.snap b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
index a00a8f3c32fb..b8bafaf65470 100644
--- a/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
+++ b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
@@ -1,6 +1,7 @@
 {
     "homo sapiens - bcf": {
         "content": [
+<<<<<<< HEAD
             {
                 "0": [
                     [
@@ -25,11 +26,23 @@
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
             }
+=======
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_filtered.vcf:md5,38f3479f9071fbe018226be0aac62354"
+                ]
+            ]
+>>>>>>> 0462840dd (Prepare for merge)
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
+<<<<<<< HEAD
         "timestamp": "2025-11-05T11:14:07.57913"
     },
     "homo sapiens - bcf - stub": {
@@ -91,11 +104,27 @@
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
             }
+=======
+        "timestamp": "2025-10-28T16:35:15.82704"
+    },
+    "homo sapiens - vcf.gz": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_filtered.vcf:md5,44659c255c5018ba2e5a3b4b80797a57"
+                ]
+            ]
+>>>>>>> 0462840dd (Prepare for merge)
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
+<<<<<<< HEAD
         "timestamp": "2025-11-05T11:14:03.41245"
     },
     "homo sapiens - vcf.gz - stub": {
@@ -190,11 +219,27 @@
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
             }
+=======
+        "timestamp": "2025-10-28T16:35:10.958678"
+    },
+    "homo sapiens - bcf.gz": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_filtered.vcf:md5,c9be02b5c5e036c25e05f59a94528203"
+                ]
+            ]
+>>>>>>> 0462840dd (Prepare for merge)
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
+<<<<<<< HEAD
         "timestamp": "2025-11-05T11:14:12.225232"
     },
     "homo sapiens - vcf": {
@@ -223,11 +268,27 @@
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
             }
+=======
+        "timestamp": "2025-10-28T16:35:21.012789"
+    },
+    "homo sapiens - vcf": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_filtered.vcf:md5,20af56305296f2b0e52979465f19804b"
+                ]
+            ]
+>>>>>>> 0462840dd (Prepare for merge)
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
+<<<<<<< HEAD
         "timestamp": "2025-11-05T11:13:59.313832"
     },
     "homo sapiens - vcf - stub": {
@@ -262,5 +323,8 @@
             "nextflow": "25.04.6"
         },
         "timestamp": "2025-11-05T11:14:15.550717"
+=======
+        "timestamp": "2025-10-28T16:35:06.185151"
+>>>>>>> 0462840dd (Prepare for merge)
     }
 }
\ No newline at end of file

From 7d199da2aadbb6b2e35f5267680c05a888b2fcab Mon Sep 17 00:00:00 2001
From: trangdo <trang.do@holzerscientific.com>
Date: Tue, 28 Oct 2025 17:10:32 +0100
Subject: [PATCH 6/8] Prepare for merge

---
 .pre-commit-config.yaml                       |  4 +-
 .../vembrane/filter/tests/main.nf.test.snap   | 64 -------------------
 2 files changed, 3 insertions(+), 65 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6f830d97d1f3..712daf3dec21 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,12 +1,13 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v3.1.0"
+    rev: "v4.0.0-alpha.8"
     hooks:
       - id: prettier
         additional_dependencies:
           - prettier@3.6.2
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
     rev: v6.0.0
     hooks:
       - id: trailing-whitespace
@@ -51,6 +52,7 @@ repos:
       - id: ruff-format # formatter
     # NOTE This runs with Docker instead of the binary. Hoping anyone messing with Dockerfiles has Docker installed
   - repo: https://github.com/hadolint/hadolint
+    rev: v2.14.0
     rev: v2.14.0
     hooks:
       - id: hadolint-docker
diff --git a/modules/nf-core/vembrane/filter/tests/main.nf.test.snap b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
index b8bafaf65470..a00a8f3c32fb 100644
--- a/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
+++ b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
@@ -1,7 +1,6 @@
 {
     "homo sapiens - bcf": {
         "content": [
-<<<<<<< HEAD
             {
                 "0": [
                     [
@@ -26,23 +25,11 @@
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
             }
-=======
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_filtered.vcf:md5,38f3479f9071fbe018226be0aac62354"
-                ]
-            ]
->>>>>>> 0462840dd (Prepare for merge)
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-<<<<<<< HEAD
         "timestamp": "2025-11-05T11:14:07.57913"
     },
     "homo sapiens - bcf - stub": {
@@ -104,27 +91,11 @@
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
             }
-=======
-        "timestamp": "2025-10-28T16:35:15.82704"
-    },
-    "homo sapiens - vcf.gz": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_filtered.vcf:md5,44659c255c5018ba2e5a3b4b80797a57"
-                ]
-            ]
->>>>>>> 0462840dd (Prepare for merge)
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-<<<<<<< HEAD
         "timestamp": "2025-11-05T11:14:03.41245"
     },
     "homo sapiens - vcf.gz - stub": {
@@ -219,27 +190,11 @@
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
             }
-=======
-        "timestamp": "2025-10-28T16:35:10.958678"
-    },
-    "homo sapiens - bcf.gz": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_filtered.vcf:md5,c9be02b5c5e036c25e05f59a94528203"
-                ]
-            ]
->>>>>>> 0462840dd (Prepare for merge)
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-<<<<<<< HEAD
         "timestamp": "2025-11-05T11:14:12.225232"
     },
     "homo sapiens - vcf": {
@@ -268,27 +223,11 @@
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
             }
-=======
-        "timestamp": "2025-10-28T16:35:21.012789"
-    },
-    "homo sapiens - vcf": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test",
-                        "single_end": false
-                    },
-                    "test_filtered.vcf:md5,20af56305296f2b0e52979465f19804b"
-                ]
-            ]
->>>>>>> 0462840dd (Prepare for merge)
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-<<<<<<< HEAD
         "timestamp": "2025-11-05T11:13:59.313832"
     },
     "homo sapiens - vcf - stub": {
@@ -323,8 +262,5 @@
             "nextflow": "25.04.6"
         },
         "timestamp": "2025-11-05T11:14:15.550717"
-=======
-        "timestamp": "2025-10-28T16:35:06.185151"
->>>>>>> 0462840dd (Prepare for merge)
     }
 }
\ No newline at end of file

From 0df82781f98edb7d6b39f05ee15515e9ab570553 Mon Sep 17 00:00:00 2001
From: dhtt <dhthutrang@gmail.com>
Date: Thu, 13 Nov 2025 14:15:16 +0100
Subject: [PATCH 7/8] Fix output extension, output name, meta.yml

---
 .pre-commit-config.yaml                       |  4 +-
 modules/nf-core/vembrane/filter/main.nf       | 38 ++++++++++-----
 modules/nf-core/vembrane/filter/meta.yml      |  9 ++--
 .../vembrane/filter/tests/main.nf.test.snap   | 48 +++++++++----------
 4 files changed, 57 insertions(+), 42 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 712daf3dec21..6f830d97d1f3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,13 +1,12 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: "v4.0.0-alpha.8"
+    rev: "v3.1.0"
     hooks:
       - id: prettier
         additional_dependencies:
           - prettier@3.6.2
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v6.0.0
     rev: v6.0.0
     hooks:
       - id: trailing-whitespace
@@ -52,7 +51,6 @@ repos:
       - id: ruff-format # formatter
     # NOTE This runs with Docker instead of the binary. Hoping anyone messing with Dockerfiles has Docker installed
   - repo: https://github.com/hadolint/hadolint
-    rev: v2.14.0
     rev: v2.14.0
     hooks:
       - id: hadolint-docker
diff --git a/modules/nf-core/vembrane/filter/main.nf b/modules/nf-core/vembrane/filter/main.nf
index 57d3869cc166..3cbd1a7cd1fc 100644
--- a/modules/nf-core/vembrane/filter/main.nf
+++ b/modules/nf-core/vembrane/filter/main.nf
@@ -1,19 +1,19 @@
 process VEMBRANE_FILTER {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/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(variant)
-    val(expression)
+    tuple val(meta), path(vcf)
+    val expression
 
     output:
-    tuple val(meta), path("*.{vcf,bcf,vcf.gz,bcf.gz}"), emit: filtered_variant
-    path "versions.yml"                               , emit: versions
+    tuple val(meta), path("*.{vcf,bcf,bcf.gz}"), emit: filtered_variant
+    path "versions.yml"                        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,13 +21,21 @@ process VEMBRANE_FILTER {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    extension = args.contains("--output-fmt vcf") || args.contains("-Ovcf") ? "vcf" :
+                    args.contains("--output-fmt bcf") || args.contains("-Obcf") ? "bcf" :
+                    args.contains("--output-fmt uncompressed-bcf") || args.contains("-Ouncompressed-bcf") ? "bcf.gz" :
+                    "vcf"
+
+    if ("${vcf}" == "${prefix}.${extension}") {
+        error("Input and output names are the same, use \"task.ext.prefix\" in module configuration to disambiguate!")
+    }
 
     """
     vembrane filter \\
         ${args} \\
         ${expression} \\
-        -o ${prefix}.filtered.vcf \\
-        ${variant}
+        -o ${prefix}.${extension} \\
+        ${vcf}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -37,9 +45,17 @@ process VEMBRANE_FILTER {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    extension = args.contains("--output-fmt vcf") || args.contains("-Ovcf") ? "vcf" :
+                    args.contains("--output-fmt bcf") || args.contains("-Obcf") ? "bcf" :
+                    args.contains("--output-fmt uncompressed-bcf") || args.contains("-Ouncompressed-bcf") ? "bcf.gz" :
+                    "vcf"
+
+    if ("${vcf}" == "${prefix}.${extension}") {
+        error("Input and output names are the same, use \"task.ext.prefix\" in module configuration to disambiguate!")
+    }
 
     """
-    touch ${prefix}.filtered.vcf
+    touch ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/vembrane/filter/meta.yml b/modules/nf-core/vembrane/filter/meta.yml
index 2d6767be23cc..1dc9d83ad135 100644
--- a/modules/nf-core/vembrane/filter/meta.yml
+++ b/modules/nf-core/vembrane/filter/meta.yml
@@ -1,6 +1,6 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "vembrane_filter"
-description: write your description here
+description: Filter VCF files with vembrane
 keywords:
   - filter
   - vcf
@@ -24,11 +24,12 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test' ]
-    - variant:
+    - vcf:
         type: file
         description: |
           Path to the VCF/BCF file to be filtered.
           e.g. 'file.vcf', 'file.vcf.gz', 'file.bcf', 'file.bcf.gz'
+        pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
         ontologies: []
   - expression:
       type: string
@@ -44,10 +45,10 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test' ]
-      - "*.{vcf,bcf,vcf.gz,bcf.gz}":
+      - "*.{vcf,bcf,bcf.gz}":
           type: file
           description: Filtered VCF output file
-          pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
+          pattern: "*.{vcf,bcf,bcf.gz}"
           ontologies: []
   versions:
     - versions.yml:
diff --git a/modules/nf-core/vembrane/filter/tests/main.nf.test.snap b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
index a00a8f3c32fb..f18e16006908 100644
--- a/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
+++ b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,6c1393e34fc3ffe763b7c75725176463"
+                        "test.vcf:md5,aaef102d56d0c3f0cdcbac7568f487fe"
                     ]
                 ],
                 "1": [
@@ -18,7 +18,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,6c1393e34fc3ffe763b7c75725176463"
+                        "test.vcf:md5,aaef102d56d0c3f0cdcbac7568f487fe"
                     ]
                 ],
                 "versions": [
@@ -30,7 +30,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-05T11:14:07.57913"
+        "timestamp": "2025-11-13T11:14:06.920892"
     },
     "homo sapiens - bcf - stub": {
         "content": [
@@ -40,7 +40,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -51,7 +51,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -63,7 +63,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-05T11:14:22.290473"
+        "timestamp": "2025-11-13T11:14:22.72139"
     },
     "homo sapiens - vcf.gz": {
         "content": [
@@ -73,7 +73,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,75cc37af6bc118370251fee6ab1532ee"
+                        "test.vcf:md5,2bb5028c50d643f0410ec3ee39979150"
                     ]
                 ],
                 "1": [
@@ -84,7 +84,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,75cc37af6bc118370251fee6ab1532ee"
+                        "test.vcf:md5,2bb5028c50d643f0410ec3ee39979150"
                     ]
                 ],
                 "versions": [
@@ -96,7 +96,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-05T11:14:03.41245"
+        "timestamp": "2025-11-13T11:14:02.397466"
     },
     "homo sapiens - vcf.gz - stub": {
         "content": [
@@ -106,7 +106,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -117,7 +117,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -129,7 +129,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-05T11:14:18.955755"
+        "timestamp": "2025-11-13T11:14:18.799085"
     },
     "homo sapiens - bcf.gz - stub": {
         "content": [
@@ -139,7 +139,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -150,7 +150,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -162,7 +162,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-05T11:14:26.669552"
+        "timestamp": "2025-11-13T11:14:26.472957"
     },
     "homo sapiens - bcf.gz": {
         "content": [
@@ -172,7 +172,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,71c159f1c953e33c94ad6fd5efbf719b"
+                        "test.vcf:md5,24a5d6b414c345ebacf5dd6270d9e4d2"
                     ]
                 ],
                 "1": [
@@ -183,7 +183,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,71c159f1c953e33c94ad6fd5efbf719b"
+                        "test.vcf:md5,24a5d6b414c345ebacf5dd6270d9e4d2"
                     ]
                 ],
                 "versions": [
@@ -195,7 +195,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-05T11:14:12.225232"
+        "timestamp": "2025-11-13T11:14:11.339463"
     },
     "homo sapiens - vcf": {
         "content": [
@@ -205,7 +205,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,116c742876dd0ab00a936178f1da9c86"
+                        "test.vcf:md5,e78b475d1d84834333b7273673530496"
                     ]
                 ],
                 "1": [
@@ -216,7 +216,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,116c742876dd0ab00a936178f1da9c86"
+                        "test.vcf:md5,e78b475d1d84834333b7273673530496"
                     ]
                 ],
                 "versions": [
@@ -228,7 +228,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-05T11:13:59.313832"
+        "timestamp": "2025-11-13T11:13:57.672228"
     },
     "homo sapiens - vcf - stub": {
         "content": [
@@ -238,7 +238,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -249,7 +249,7 @@
                         {
                             "id": "test"
                         },
-                        "test.filtered.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -261,6 +261,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-05T11:14:15.550717"
+        "timestamp": "2025-11-13T11:14:15.063118"
     }
 }
\ No newline at end of file

From 6ac59f88e91dca6594145f941034808aeb5880c6 Mon Sep 17 00:00:00 2001
From: dhtt <dhthutrang@gmail.com>
Date: Wed, 19 Nov 2025 13:14:07 +0100
Subject: [PATCH 8/8] Minor fixes in snapshot test, main & meta output

---
 modules/nf-core/vembrane/filter/main.nf       |  2 +-
 modules/nf-core/vembrane/filter/meta.yml      |  2 +-
 .../vembrane/filter/tests/main.nf.test        | 36 +++++++---
 .../vembrane/filter/tests/main.nf.test.snap   | 72 ++++++++++++++-----
 4 files changed, 86 insertions(+), 26 deletions(-)

diff --git a/modules/nf-core/vembrane/filter/main.nf b/modules/nf-core/vembrane/filter/main.nf
index 3cbd1a7cd1fc..5df75fe7d302 100644
--- a/modules/nf-core/vembrane/filter/main.nf
+++ b/modules/nf-core/vembrane/filter/main.nf
@@ -12,7 +12,7 @@ process VEMBRANE_FILTER {
     val expression
 
     output:
-    tuple val(meta), path("*.{vcf,bcf,bcf.gz}"), emit: filtered_variant
+    tuple val(meta), path("*.{vcf,bcf,bcf.gz}"), emit: vcf
     path "versions.yml"                        , emit: versions
 
     when:
diff --git a/modules/nf-core/vembrane/filter/meta.yml b/modules/nf-core/vembrane/filter/meta.yml
index 1dc9d83ad135..7e654a3ff6a7 100644
--- a/modules/nf-core/vembrane/filter/meta.yml
+++ b/modules/nf-core/vembrane/filter/meta.yml
@@ -39,7 +39,7 @@ input:
       ontologies: []
 
 output:
-  filtered_variant:
+  vcf:
     - - meta:
           type: map
           description: |
diff --git a/modules/nf-core/vembrane/filter/tests/main.nf.test b/modules/nf-core/vembrane/filter/tests/main.nf.test
index dff81dc5ea00..c5c2ebbb3773 100644
--- a/modules/nf-core/vembrane/filter/tests/main.nf.test
+++ b/modules/nf-core/vembrane/filter/tests/main.nf.test
@@ -26,7 +26,10 @@ 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 +52,8 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out
+                    process.out,
+                    path(process.out.versions[0]).yaml
                     ).match() }
             )
         }
@@ -72,7 +76,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
 
@@ -94,7 +101,10 @@ test("homo sapiens - bcf.gz") {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
 
@@ -119,7 +129,10 @@ test("homo sapiens - bcf.gz") {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
             )
         }
 
@@ -145,7 +158,8 @@ test("homo sapiens - bcf.gz") {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out
+                    process.out,
+                    path(process.out.versions[0]).yaml
                     ).match() }
             )
         }
@@ -171,7 +185,10 @@ test("homo sapiens - bcf.gz") {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                    ).match() }
             )
         }
 
@@ -196,7 +213,10 @@ test("homo sapiens - bcf.gz - stub") {
         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/filter/tests/main.nf.test.snap b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
index f18e16006908..1afce22f4eb0 100644
--- a/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
+++ b/modules/nf-core/vembrane/filter/tests/main.nf.test.snap
@@ -13,7 +13,7 @@
                 "1": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ],
-                "filtered_variant": [
+                "vcf": [
                     [
                         {
                             "id": "test"
@@ -24,13 +24,18 @@
                 "versions": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
+            },
+            {
+                "VEMBRANE_FILTER": {
+                    "vembrane": "2.4.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-13T11:14:06.920892"
+        "timestamp": "2025-11-19T13:01:08.406479"
     },
     "homo sapiens - bcf - stub": {
         "content": [
@@ -46,7 +51,7 @@
                 "1": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ],
-                "filtered_variant": [
+                "vcf": [
                     [
                         {
                             "id": "test"
@@ -57,13 +62,18 @@
                 "versions": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
+            },
+            {
+                "VEMBRANE_FILTER": {
+                    "vembrane": "2.4.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-13T11:14:22.72139"
+        "timestamp": "2025-11-19T13:02:01.86051"
     },
     "homo sapiens - vcf.gz": {
         "content": [
@@ -79,7 +89,7 @@
                 "1": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ],
-                "filtered_variant": [
+                "vcf": [
                     [
                         {
                             "id": "test"
@@ -90,13 +100,18 @@
                 "versions": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
+            },
+            {
+                "VEMBRANE_FILTER": {
+                    "vembrane": "2.4.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-13T11:14:02.397466"
+        "timestamp": "2025-11-19T13:00:53.748275"
     },
     "homo sapiens - vcf.gz - stub": {
         "content": [
@@ -112,7 +127,7 @@
                 "1": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ],
-                "filtered_variant": [
+                "vcf": [
                     [
                         {
                             "id": "test"
@@ -123,13 +138,18 @@
                 "versions": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
+            },
+            {
+                "VEMBRANE_FILTER": {
+                    "vembrane": "2.4.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-13T11:14:18.799085"
+        "timestamp": "2025-11-19T13:01:48.889571"
     },
     "homo sapiens - bcf.gz - stub": {
         "content": [
@@ -145,7 +165,7 @@
                 "1": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ],
-                "filtered_variant": [
+                "vcf": [
                     [
                         {
                             "id": "test"
@@ -156,13 +176,18 @@
                 "versions": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
+            },
+            {
+                "VEMBRANE_FILTER": {
+                    "vembrane": "2.4.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-13T11:14:26.472957"
+        "timestamp": "2025-11-19T13:02:16.104571"
     },
     "homo sapiens - bcf.gz": {
         "content": [
@@ -178,7 +203,7 @@
                 "1": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ],
-                "filtered_variant": [
+                "vcf": [
                     [
                         {
                             "id": "test"
@@ -189,13 +214,18 @@
                 "versions": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
+            },
+            {
+                "VEMBRANE_FILTER": {
+                    "vembrane": "2.4.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-13T11:14:11.339463"
+        "timestamp": "2025-11-19T13:01:23.162816"
     },
     "homo sapiens - vcf": {
         "content": [
@@ -211,7 +241,7 @@
                 "1": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ],
-                "filtered_variant": [
+                "vcf": [
                     [
                         {
                             "id": "test"
@@ -222,13 +252,18 @@
                 "versions": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
+            },
+            {
+                "VEMBRANE_FILTER": {
+                    "vembrane": "2.4.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-13T11:13:57.672228"
+        "timestamp": "2025-11-19T13:00:38.636223"
     },
     "homo sapiens - vcf - stub": {
         "content": [
@@ -244,7 +279,7 @@
                 "1": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ],
-                "filtered_variant": [
+                "vcf": [
                     [
                         {
                             "id": "test"
@@ -255,12 +290,17 @@
                 "versions": [
                     "versions.yml:md5,16c0e3eafdc08317b2a50616f2425a85"
                 ]
+            },
+            {
+                "VEMBRANE_FILTER": {
+                    "vembrane": "2.4.0"
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-13T11:14:15.063118"
+        "timestamp": "2025-11-19T13:01:34.578017"
     }
 }
\ No newline at end of file