From 3c56c6494299d8a920a2a9294564573850f65bad Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Wed, 19 Nov 2025 15:23:01 -0800
Subject: [PATCH 01/16] add whatshap phase module

---
 .../nf-core/whatshap/phase/environment.yml    |   7 ++
 modules/nf-core/whatshap/phase/main.nf        |  56 ++++++++++
 modules/nf-core/whatshap/phase/meta.yml       |  97 +++++++++++++++++
 .../nf-core/whatshap/phase/tests/main.nf.test | 102 ++++++++++++++++++
 .../whatshap/phase/tests/main.nf.test.snap    |  51 +++++++++
 5 files changed, 313 insertions(+)
 create mode 100644 modules/nf-core/whatshap/phase/environment.yml
 create mode 100644 modules/nf-core/whatshap/phase/main.nf
 create mode 100644 modules/nf-core/whatshap/phase/meta.yml
 create mode 100644 modules/nf-core/whatshap/phase/tests/main.nf.test
 create mode 100644 modules/nf-core/whatshap/phase/tests/main.nf.test.snap

diff --git a/modules/nf-core/whatshap/phase/environment.yml b/modules/nf-core/whatshap/phase/environment.yml
new file mode 100644
index 00000000000..389d6871ef4
--- /dev/null
+++ b/modules/nf-core/whatshap/phase/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::whatshap=2.8"
diff --git a/modules/nf-core/whatshap/phase/main.nf b/modules/nf-core/whatshap/phase/main.nf
new file mode 100644
index 00000000000..b4f60602e2a
--- /dev/null
+++ b/modules/nf-core/whatshap/phase/main.nf
@@ -0,0 +1,56 @@
+process WHATSHAP_PHASE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/whatshap:2.8--c3862a4b2ad0f978':
+        'community.wave.seqera.io/library/whatshap:2.8--7fe530bc624a3e5a' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi)
+    tuple val(meta2), path(bam), path(bai)
+    tuple val(meta3), path(fasta), path(fai)
+
+    output:
+    tuple val(meta), path("*.phased.vcf.gz")    , emit: vcf
+    tuple val(meta), path("*.phased.vcf.gz.tbi"), emit: tbi
+    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}"
+    """
+    whatshap \\
+        phase \\
+        --output ${prefix}.phased.vcf \\
+        --reference $fasta \\
+        $args \\
+        $vcf \\
+        $bam
+
+    bgzip ${prefix}.phased.vcf
+    tabix -p vcf ${prefix}.phased.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        whatshap: \$(whatshap --version 2>&1 | sed 's/whatshap //g')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.phased.vcf.gz
+    touch ${prefix}.phased.vcf.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        whatshap: \$(whatshap --version 2>&1 | sed 's/whatshap //g')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/whatshap/phase/meta.yml b/modules/nf-core/whatshap/phase/meta.yml
new file mode 100644
index 00000000000..148a5462a58
--- /dev/null
+++ b/modules/nf-core/whatshap/phase/meta.yml
@@ -0,0 +1,97 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "whatshap_phase"
+description: Phase variants in a VCF file using long-read sequencing data
+keywords:
+  - phasing
+  - haplotypes
+  - vcf
+  - long-reads
+  - nanopore
+  - pacbio
+tools:
+  - whatshap:
+      description: |
+        WhatsHap is a software for phasing genomic variants using DNA sequencing
+        reads, also called read-based phasing or haplotype assembly.
+      homepage: https://whatshap.readthedocs.io/
+      documentation: https://whatshap.readthedocs.io/
+      tool_dev_url: https://github.com/whatshap/whatshap
+      doi: "10.1101/085050"
+      licence: ["MIT"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - vcf:
+        type: file
+        description: VCF file with unphased variants (can be gzipped)
+        pattern: "*.{vcf,vcf.gz}"
+    - tbi:
+        type: file
+        description: VCF index file (optional but recommended)
+        pattern: "*.{tbi,csi}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing bam information
+          e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM file with aligned reads
+        pattern: "*.bam"
+    - bai:
+        type: file
+        description: BAM index file (optional but recommended)
+        pattern: "*.bai"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. [ id:'genome' ]
+    - fasta:
+        type: file
+        description: Reference genome in FASTA format
+        pattern: "*.{fa,fasta}"
+    - fai:
+        type: file
+        description: Reference genome index
+        pattern: "*.fai"
+
+output:
+  vcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.phased.vcf.gz":
+          type: file
+          description: Bgzipped phased VCF file
+          pattern: "*.vcf.gz"
+          ontologies: []
+  tbi:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.phased.vcf.gz.tbi":
+          type: file
+          description: Phased VCF index file
+          pattern: "*.vcf.gz"
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+
+authors:
+  - "@haidyi"
+maintainers:
+  - "@haidyi"
diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test b/modules/nf-core/whatshap/phase/tests/main.nf.test
new file mode 100644
index 00000000000..a3f08ca0953
--- /dev/null
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test
@@ -0,0 +1,102 @@
+nextflow_process {
+
+    name "Test Process WHATSHAP_PHASE"
+    script "../main.nf"
+    process "WHATSHAP_PHASE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "whatshap"
+    tag "whatshap/phase"
+    tag "samtools_faidx"
+
+    setup {
+        run("SAMTOOLS_FAIDX") {
+            script "../../../samtools/faidx/main.nf"
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true) ]
+                input[1] = [[],[]]
+                input[2] = false
+                """
+            }
+        }
+    }
+
+    test("whatshap - phase - vcf") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/NA03697B2_new.pbmm2.repeats.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/NA03697B2_new.pbmm2.repeats.vcf.gz.csi', checkIfExists: true),
+
+                ]
+
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam.bai', checkIfExists: true),
+                ]
+
+                input[2] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true)
+                ]).join(SAMTOOLS_FAIDX.out.fai)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.vcf[0][1]).vcf.summary,
+                    file(process.out.vcf[0][1]).vcf.variantsMD5,
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("whatshap - phase - vcf - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/NA03697B2_new.pbmm2.repeats.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/vcf/NA03697B2_new.pbmm2.repeats.vcf.gz.csi', checkIfExists: true),
+
+                ]
+
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/NA03697B2_downsampled.pbmm2.repeats.bam.bai', checkIfExists: true),
+                ]
+
+                input[2] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome3.fasta', checkIfExists: true)
+                ]).join(SAMTOOLS_FAIDX.out.fai)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
new file mode 100644
index 00000000000..23a8d73ee8e
--- /dev/null
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
@@ -0,0 +1,51 @@
+{
+    "whatshap - phase - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "/Users/hyi/Documents/proj/modules/.nf-test/tests/e287a32825e762a59103c13d3c316644/work/38/14e6fb7a2d6c8765594e1a3d7a9cf7/test.phased.vcf.gz"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "/Users/hyi/Documents/proj/modules/.nf-test/tests/e287a32825e762a59103c13d3c316644/work/38/14e6fb7a2d6c8765594e1a3d7a9cf7/test.phased.vcf.gz"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.2"
+        },
+        "timestamp": "2025-11-19T15:19:22.827299"
+    }
+}
\ No newline at end of file

From cba565faa413b64fa6e897430f01aca20d525e96 Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Wed, 19 Nov 2025 17:36:15 -0600
Subject: [PATCH 02/16] change the vcf-specific test

---
 modules/nf-core/whatshap/phase/tests/main.nf.test     |  4 ++--
 .../nf-core/whatshap/phase/tests/main.nf.test.snap    | 11 +++++++++++
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test b/modules/nf-core/whatshap/phase/tests/main.nf.test
index a3f08ca0953..9ede19d35aa 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test
@@ -54,8 +54,8 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    file(process.out.vcf[0][1]).vcf.summary,
-                    file(process.out.vcf[0][1]).vcf.variantsMD5,
+                    path(process.out.vcf.get(0).get(1)).vcf.summary,
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
                     ).match() }
             )
         }
diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
index 23a8d73ee8e..6b2d331be55 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
@@ -47,5 +47,16 @@
             "nextflow": "25.04.2"
         },
         "timestamp": "2025-11-19T15:19:22.827299"
+    },
+    "whatshap - phase - vcf": {
+        "content": [
+            "VcfFile [chromosomes=[chr19:45760000-45770300], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]",
+            "e75d1ebbe87d6e55739cacb4e81dcd08"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-11-19T17:33:13.304122613"
     }
 }
\ No newline at end of file

From 9ae34b7f10f907d5f85ea150361c173a19aec340 Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Wed, 19 Nov 2025 18:09:52 -0600
Subject: [PATCH 03/16] change test

---
 .../nf-core/whatshap/phase/tests/main.nf.test |  3 +-
 .../whatshap/phase/tests/main.nf.test.snap    | 49 -------------------
 2 files changed, 1 insertion(+), 51 deletions(-)

diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test b/modules/nf-core/whatshap/phase/tests/main.nf.test
index 9ede19d35aa..a67d2e46ecf 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test
@@ -92,8 +92,7 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert process.success }
             )
         }
 
diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
index 6b2d331be55..37c64ea38eb 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
@@ -1,53 +1,4 @@
 {
-    "whatshap - phase - vcf - stub": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "/Users/hyi/Documents/proj/modules/.nf-test/tests/e287a32825e762a59103c13d3c316644/work/38/14e6fb7a2d6c8765594e1a3d7a9cf7/test.phased.vcf.gz"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
-                ],
-                "tbi": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "/Users/hyi/Documents/proj/modules/.nf-test/tests/e287a32825e762a59103c13d3c316644/work/38/14e6fb7a2d6c8765594e1a3d7a9cf7/test.phased.vcf.gz"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
-        },
-        "timestamp": "2025-11-19T15:19:22.827299"
-    },
     "whatshap - phase - vcf": {
         "content": [
             "VcfFile [chromosomes=[chr19:45760000-45770300], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]",

From 8b7b28e33d80917302ea6e2c40589ca09e68b534 Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Wed, 19 Nov 2025 18:18:56 -0600
Subject: [PATCH 04/16] add versions

---
 modules/nf-core/whatshap/phase/tests/main.nf.test | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test b/modules/nf-core/whatshap/phase/tests/main.nf.test
index a67d2e46ecf..e9d18b9ab37 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test
@@ -8,7 +8,7 @@ nextflow_process {
     tag "modules_nfcore"
     tag "whatshap"
     tag "whatshap/phase"
-    tag "samtools_faidx"
+    tag "samtools/faidx"
 
     setup {
         run("SAMTOOLS_FAIDX") {
@@ -56,6 +56,7 @@ nextflow_process {
                 { assert snapshot(
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.versions,
                     ).match() }
             )
         }

From 5f4e5f9729c45680e33038e5ced186030b5df1b8 Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Wed, 19 Nov 2025 18:20:21 -0600
Subject: [PATCH 05/16] remove snapshot

---
 .../nf-core/whatshap/phase/tests/main.nf.test.snap  | 13 -------------
 1 file changed, 13 deletions(-)
 delete mode 100644 modules/nf-core/whatshap/phase/tests/main.nf.test.snap

diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
deleted file mode 100644
index 37c64ea38eb..00000000000
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
+++ /dev/null
@@ -1,13 +0,0 @@
-{
-    "whatshap - phase - vcf": {
-        "content": [
-            "VcfFile [chromosomes=[chr19:45760000-45770300], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]",
-            "e75d1ebbe87d6e55739cacb4e81dcd08"
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-11-19T17:33:13.304122613"
-    }
-}
\ No newline at end of file

From 3e8877d64ae0b96de3ee2142fc2ea331826e21a8 Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Wed, 19 Nov 2025 18:26:43 -0600
Subject: [PATCH 06/16] update snapshot

---
 .../whatshap/phase/tests/main.nf.test.snap       | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 modules/nf-core/whatshap/phase/tests/main.nf.test.snap

diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
new file mode 100644
index 00000000000..00ecb0968eb
--- /dev/null
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
@@ -0,0 +1,16 @@
+{
+    "whatshap - phase - vcf": {
+        "content": [
+            "VcfFile [chromosomes=[chr19:45760000-45770300], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]",
+            "e75d1ebbe87d6e55739cacb4e81dcd08",
+            [
+                "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-11-19T18:25:34.024894349"
+    }
+}
\ No newline at end of file

From 42850a647cb8f6d5d6d83b1ccf280c7960c69685 Mon Sep 17 00:00:00 2001
From: HD Yi <haidongyi@gmail.com>
Date: Mon, 24 Nov 2025 09:21:54 -0800
Subject: [PATCH 07/16] Update
 modules/nf-core/whatshap/phase/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/whatshap/phase/tests/main.nf.test | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test b/modules/nf-core/whatshap/phase/tests/main.nf.test
index e9d18b9ab37..ed1d3df5668 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test
@@ -57,6 +57,7 @@ nextflow_process {
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
                     process.out.versions,
+                    path(process.out.versions[0]).yaml,
                     ).match() }
             )
         }

From 3a6669eb54a012323dd9cd82963a9ed1952ea79d Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Mon, 24 Nov 2025 11:52:11 -0600
Subject: [PATCH 08/16] rm unused args

---
 modules/nf-core/whatshap/phase/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/whatshap/phase/main.nf b/modules/nf-core/whatshap/phase/main.nf
index b4f60602e2a..bc166a2064f 100644
--- a/modules/nf-core/whatshap/phase/main.nf
+++ b/modules/nf-core/whatshap/phase/main.nf
@@ -42,7 +42,6 @@ process WHATSHAP_PHASE {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.phased.vcf.gz

From da323149905c84609703e57f2e8bb3fad5e14a72 Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Mon, 24 Nov 2025 11:52:34 -0600
Subject: [PATCH 09/16] add snapshot

---
 .../nf-core/whatshap/phase/tests/main.nf.test |  4 +-
 .../whatshap/phase/tests/main.nf.test.snap    | 49 +++++++++++++++++++
 2 files changed, 51 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test b/modules/nf-core/whatshap/phase/tests/main.nf.test
index ed1d3df5668..622a91237ba 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test
@@ -56,7 +56,6 @@ nextflow_process {
                 { assert snapshot(
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
-                    process.out.versions,
                     path(process.out.versions[0]).yaml,
                     ).match() }
             )
@@ -94,7 +93,8 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert process.success }
+                { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
index 00ecb0968eb..4c3f575e336 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
@@ -1,4 +1,53 @@
 {
+    "whatshap - phase - vcf - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "/home/hyi/proj/modules/.nf-test/tests/7e4bcbe39c49c581a6da5ac23f7380c9/work/d0/80a77469a6d95b50348c3d6068d0c3/test.phased.vcf.gz"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "/home/hyi/proj/modules/.nf-test/tests/7e4bcbe39c49c581a6da5ac23f7380c9/work/d0/80a77469a6d95b50348c3d6068d0c3/test.phased.vcf.gz"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-11-24T11:48:27.220260344"
+    },
     "whatshap - phase - vcf": {
         "content": [
             "VcfFile [chromosomes=[chr19:45760000-45770300], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]",

From 1bb901113dad83506de367fb0c45cba7e298f9ec Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Mon, 24 Nov 2025 11:52:41 -0600
Subject: [PATCH 10/16] add ontologies

---
 modules/nf-core/whatshap/phase/meta.yml | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/whatshap/phase/meta.yml b/modules/nf-core/whatshap/phase/meta.yml
index 148a5462a58..05dbbf5fb38 100644
--- a/modules/nf-core/whatshap/phase/meta.yml
+++ b/modules/nf-core/whatshap/phase/meta.yml
@@ -70,8 +70,9 @@ output:
       - "*.phased.vcf.gz":
           type: file
           description: Bgzipped phased VCF file
-          pattern: "*.vcf.gz"
-          ontologies: []
+          pattern: "*.phased.vcf.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
   tbi:
     - - meta:
           type: map
@@ -81,8 +82,9 @@ output:
       - "*.phased.vcf.gz.tbi":
           type: file
           description: Phased VCF index file
-          pattern: "*.vcf.gz"
-          ontologies: []
+          pattern: "*.phased.vcf.gz.tbi"
+          ontologies:
+            - edam: http://edamontology.org/format_3616 # TBI format
   versions:
     - versions.yml:
         type: file

From 750d314c7dd19bb00ea75e66d3c66ecb173e33a6 Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Mon, 24 Nov 2025 12:20:22 -0600
Subject: [PATCH 11/16] update the snapshot

---
 .../nf-core/whatshap/phase/tests/main.nf.test |  5 +-
 .../whatshap/phase/tests/main.nf.test.snap    | 61 ++++++-------------
 2 files changed, 22 insertions(+), 44 deletions(-)

diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test b/modules/nf-core/whatshap/phase/tests/main.nf.test
index 622a91237ba..2555c8c9152 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test
@@ -94,7 +94,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+                    process.out.tbi,
+                    path(process.out.versions[0]).yaml
+                    ).match() }
             )
         }
 
diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
index 4c3f575e336..51162cf40c0 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
@@ -1,65 +1,40 @@
 {
     "whatshap - phase - vcf - stub": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "/home/hyi/proj/modules/.nf-test/tests/7e4bcbe39c49c581a6da5ac23f7380c9/work/d0/80a77469a6d95b50348c3d6068d0c3/test.phased.vcf.gz"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
-                ],
-                "tbi": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "/home/hyi/proj/modules/.nf-test/tests/7e4bcbe39c49c581a6da5ac23f7380c9/work/d0/80a77469a6d95b50348c3d6068d0c3/test.phased.vcf.gz"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
+            ],
+            {
+                "WHATSHAP_PHASE": {
+                    "whatshap": 2.8
+                }
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-24T11:48:27.220260344"
+        "timestamp": "2025-11-24T12:18:25.956894074"
     },
     "whatshap - phase - vcf": {
         "content": [
             "VcfFile [chromosomes=[chr19:45760000-45770300], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]",
             "e75d1ebbe87d6e55739cacb4e81dcd08",
-            [
-                "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
-            ]
+            {
+                "WHATSHAP_PHASE": {
+                    "whatshap": 2.8
+                }
+            }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-19T18:25:34.024894349"
+        "timestamp": "2025-11-24T12:18:21.776294793"
     }
 }
\ No newline at end of file

From cf6027ff0c2a9a17124257b83a56913b5e21dc40 Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Mon, 24 Nov 2025 12:26:16 -0600
Subject: [PATCH 12/16] add versions to snapshot

---
 modules/nf-core/whatshap/phase/tests/main.nf.test      |  2 ++
 modules/nf-core/whatshap/phase/tests/main.nf.test.snap | 10 ++++++++--
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test b/modules/nf-core/whatshap/phase/tests/main.nf.test
index 2555c8c9152..27c68a669fd 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test
@@ -56,6 +56,7 @@ nextflow_process {
                 { assert snapshot(
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.versions,
                     path(process.out.versions[0]).yaml,
                     ).match() }
             )
@@ -96,6 +97,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.tbi,
+                    process.out.versions,
                     path(process.out.versions[0]).yaml
                     ).match() }
             )
diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
index 51162cf40c0..b406e34ed82 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
@@ -9,6 +9,9 @@
                     "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ]
             ],
+            [
+                "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
+            ],
             {
                 "WHATSHAP_PHASE": {
                     "whatshap": 2.8
@@ -19,12 +22,15 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-24T12:18:25.956894074"
+        "timestamp": "2025-11-24T12:25:06.255615822"
     },
     "whatshap - phase - vcf": {
         "content": [
             "VcfFile [chromosomes=[chr19:45760000-45770300], sampleCount=1, variantCount=1, phased=false, phasedAutodetect=false]",
             "e75d1ebbe87d6e55739cacb4e81dcd08",
+            [
+                "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
+            ],
             {
                 "WHATSHAP_PHASE": {
                     "whatshap": 2.8
@@ -35,6 +41,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-11-24T12:18:21.776294793"
+        "timestamp": "2025-11-24T12:25:02.040845428"
     }
 }
\ No newline at end of file

From 7f4c53878fb7a8f3e28ae9756b9d877a38e047f9 Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Thu, 4 Dec 2025 13:12:17 -0600
Subject: [PATCH 13/16] fix stub issues

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

diff --git a/modules/nf-core/whatshap/phase/main.nf b/modules/nf-core/whatshap/phase/main.nf
index bc166a2064f..4517a9cd3b6 100644
--- a/modules/nf-core/whatshap/phase/main.nf
+++ b/modules/nf-core/whatshap/phase/main.nf
@@ -44,7 +44,7 @@ process WHATSHAP_PHASE {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.phased.vcf.gz
+    echo "" | gzip > ${prefix}.phased.vcf.gz
     touch ${prefix}.phased.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml

From 4a179d06d571eb9fa0a47e683cc47089b955acc5 Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Thu, 4 Dec 2025 13:12:29 -0600
Subject: [PATCH 14/16] update the test and snap

---
 .../nf-core/whatshap/phase/tests/main.nf.test |  6 +-
 .../whatshap/phase/tests/main.nf.test.snap    | 64 +++++++++++++------
 2 files changed, 45 insertions(+), 25 deletions(-)

diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test b/modules/nf-core/whatshap/phase/tests/main.nf.test
index 27c68a669fd..5d6ec2b8a9e 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test
@@ -95,11 +95,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    process.out.tbi,
-                    process.out.versions,
-                    path(process.out.versions[0]).yaml
-                    ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
index b406e34ed82..2d0b696d0b7 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
@@ -1,28 +1,52 @@
 {
     "whatshap - phase - vcf - stub": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ]
-            ],
-            [
-                "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
-            ],
             {
-                "WHATSHAP_PHASE": {
-                    "whatshap": 2.8
-                }
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.phased.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.phased.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,eebecfb3d7f284fc7d11c67978bf1994"
+                ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-24T12:25:06.255615822"
+        "timestamp": "2025-12-04T13:11:14.419732725"
     },
     "whatshap - phase - vcf": {
         "content": [
@@ -38,9 +62,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-11-24T12:25:02.040845428"
+        "timestamp": "2025-12-04T13:11:09.397108709"
     }
 }
\ No newline at end of file

From 27072daafbf0cecda6f3b92d7ff97d4d907ab523 Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Thu, 4 Dec 2025 13:15:15 -0600
Subject: [PATCH 15/16] fix format with "nextflow lint"

---
 modules/nf-core/whatshap/phase/main.nf | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/modules/nf-core/whatshap/phase/main.nf b/modules/nf-core/whatshap/phase/main.nf
index 4517a9cd3b6..b114b8e6f52 100644
--- a/modules/nf-core/whatshap/phase/main.nf
+++ b/modules/nf-core/whatshap/phase/main.nf
@@ -1,11 +1,11 @@
 process WHATSHAP_PHASE {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/whatshap:2.8--c3862a4b2ad0f978':
-        'community.wave.seqera.io/library/whatshap:2.8--7fe530bc624a3e5a' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'oras://community.wave.seqera.io/library/whatshap:2.8--c3862a4b2ad0f978'
+        : 'community.wave.seqera.io/library/whatshap:2.8--7fe530bc624a3e5a'}"
 
     input:
     tuple val(meta), path(vcf), path(tbi)
@@ -13,9 +13,9 @@ process WHATSHAP_PHASE {
     tuple val(meta3), path(fasta), path(fai)
 
     output:
-    tuple val(meta), path("*.phased.vcf.gz")    , emit: vcf
+    tuple val(meta), path("*.phased.vcf.gz"), emit: vcf
     tuple val(meta), path("*.phased.vcf.gz.tbi"), emit: tbi
-    path "versions.yml"                         , emit: versions
+    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,10 +27,10 @@ process WHATSHAP_PHASE {
     whatshap \\
         phase \\
         --output ${prefix}.phased.vcf \\
-        --reference $fasta \\
-        $args \\
-        $vcf \\
-        $bam
+        --reference ${fasta} \\
+        ${args} \\
+        ${vcf} \\
+        ${bam}
 
     bgzip ${prefix}.phased.vcf
     tabix -p vcf ${prefix}.phased.vcf.gz

From 995b9114c0e794ea3ab1624a0c446a3fd659108c Mon Sep 17 00:00:00 2001
From: HaidYi <haidongyi@gmail.com>
Date: Mon, 8 Dec 2025 10:19:05 -0600
Subject: [PATCH 16/16] fix hardcoded name and file name ambiguity problem

---
 modules/nf-core/whatshap/phase/main.nf        | 22 +++++++++++++------
 modules/nf-core/whatshap/phase/meta.yml       |  8 +++----
 .../whatshap/phase/tests/main.nf.test.snap    | 12 +++++-----
 3 files changed, 25 insertions(+), 17 deletions(-)

diff --git a/modules/nf-core/whatshap/phase/main.nf b/modules/nf-core/whatshap/phase/main.nf
index b114b8e6f52..6d572960783 100644
--- a/modules/nf-core/whatshap/phase/main.nf
+++ b/modules/nf-core/whatshap/phase/main.nf
@@ -13,8 +13,8 @@ process WHATSHAP_PHASE {
     tuple val(meta3), path(fasta), path(fai)
 
     output:
-    tuple val(meta), path("*.phased.vcf.gz"), emit: vcf
-    tuple val(meta), path("*.phased.vcf.gz.tbi"), emit: tbi
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi
     path "versions.yml", emit: versions
 
     when:
@@ -23,17 +23,21 @@ process WHATSHAP_PHASE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+
+    if ("${vcf}" == "${prefix}.vcf" || "${vcf}" == "${prefix}.vcf.gz") {
+        error("Input and output names are the same, set prefix in module configuration to disambiguate!")
+    }
     """
     whatshap \\
         phase \\
-        --output ${prefix}.phased.vcf \\
+        --output ${prefix}.vcf \\
         --reference ${fasta} \\
         ${args} \\
         ${vcf} \\
         ${bam}
 
-    bgzip ${prefix}.phased.vcf
-    tabix -p vcf ${prefix}.phased.vcf.gz
+    bgzip ${prefix}.vcf
+    tabix -p vcf ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -43,9 +47,13 @@ process WHATSHAP_PHASE {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+
+    if ("${vcf}" == "${prefix}.vcf" || "${vcf}" == "${prefix}.vcf.gz") {
+        error("Input and output names are the same, set prefix in module configuration to disambiguate!")
+    }
     """
-    echo "" | gzip > ${prefix}.phased.vcf.gz
-    touch ${prefix}.phased.vcf.gz.tbi
+    echo "" | gzip > ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/whatshap/phase/meta.yml b/modules/nf-core/whatshap/phase/meta.yml
index 05dbbf5fb38..89233aae3b6 100644
--- a/modules/nf-core/whatshap/phase/meta.yml
+++ b/modules/nf-core/whatshap/phase/meta.yml
@@ -67,10 +67,10 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - "*.phased.vcf.gz":
+      - "*.vcf.gz":
           type: file
           description: Bgzipped phased VCF file
-          pattern: "*.phased.vcf.gz"
+          pattern: "*.vcf.gz"
           ontologies:
             - edam: http://edamontology.org/format_3989 # GZIP format
   tbi:
@@ -79,10 +79,10 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - "*.phased.vcf.gz.tbi":
+      - "*.vcf.gz.tbi":
           type: file
           description: Phased VCF index file
-          pattern: "*.phased.vcf.gz.tbi"
+          pattern: "*.vcf.gz.tbi"
           ontologies:
             - edam: http://edamontology.org/format_3616 # TBI format
   versions:
diff --git a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
index 2d0b696d0b7..18b00f7fb6b 100644
--- a/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
+++ b/modules/nf-core/whatshap/phase/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "test.phased.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "1": [
@@ -15,7 +15,7 @@
                         {
                             "id": "test"
                         },
-                        "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
@@ -26,7 +26,7 @@
                         {
                             "id": "test"
                         },
-                        "test.phased.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "vcf": [
@@ -34,7 +34,7 @@
                         {
                             "id": "test"
                         },
-                        "test.phased.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions": [
@@ -46,7 +46,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-04T13:11:14.419732725"
+        "timestamp": "2025-12-08T10:09:39.439411781"
     },
     "whatshap - phase - vcf": {
         "content": [
@@ -65,6 +65,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-04T13:11:09.397108709"
+        "timestamp": "2025-12-08T10:09:34.591009388"
     }
 }
\ No newline at end of file