From 03634e416087a394046a7fcfd5c5f76bbf9f10ee Mon Sep 17 00:00:00 2001
From: Kiran <kirankchari@gmail.com>
Date: Fri, 29 May 2026 15:52:31 +0800
Subject: [PATCH 01/12] feat: add varnet module

---
 modules/nf-core/varnet/main.nf                |  68 ++++++++
 modules/nf-core/varnet/meta.yml               | 158 ++++++++++++++++++
 modules/nf-core/varnet/tests/main.nf.test     |  97 +++++++++++
 .../nf-core/varnet/tests/main.nf.test.snap    |  46 +++++
 modules/nf-core/varnet/tests/nextflow.config  |   8 +
 5 files changed, 377 insertions(+)
 create mode 100644 modules/nf-core/varnet/main.nf
 create mode 100644 modules/nf-core/varnet/meta.yml
 create mode 100644 modules/nf-core/varnet/tests/main.nf.test
 create mode 100644 modules/nf-core/varnet/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/varnet/tests/nextflow.config

diff --git a/modules/nf-core/varnet/main.nf b/modules/nf-core/varnet/main.nf
new file mode 100644
index 000000000000..dc3678510f81
--- /dev/null
+++ b/modules/nf-core/varnet/main.nf
@@ -0,0 +1,68 @@
+process VARNET {
+    tag "$meta.id"
+    label 'process_high_memory'
+
+    // Using the official VarNet Docker image
+    container "docker.io/kiranchari/varnet:latest"
+
+    input:
+    tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor)
+    tuple val(meta2), path(intervals)
+    tuple val(meta3), path(fasta)
+    tuple val(meta4), path(fai)
+
+    output:
+    tuple val(meta), path("${prefix}/${prefix}.vcf.gz")    , emit: vcf
+    tuple val("${task.process}"), val("varnet"), val("1.0.0"), emit: versions, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def regions = intervals ? "--region_bed \$WORKDIR/${intervals}" : ""
+    def normal  = input_normal ? "--normal_bam \$WORKDIR/${input_normal}" : ""
+    """
+
+    WORKDIR=\$(pwd)
+
+    cd /VarNet
+    TF_CPP_MIN_LOG_LEVEL=3 python /VarNet/filter.py \\
+        --sample_name ${prefix} \\
+        ${normal} \\
+        --tumor_bam \$WORKDIR/${input_tumor} \\
+        --reference \$WORKDIR/${fasta} \\
+        --output_dir \$WORKDIR \\
+        --processes ${task.cpus} \\
+        ${regions} \\
+        ${args}
+
+    TF_CPP_MIN_LOG_LEVEL=3 python /VarNet/predict.py \\
+        --sample_name ${prefix} \\
+        ${normal} \\
+        --tumor_bam \$WORKDIR/${input_tumor} \\
+        --reference \$WORKDIR/${fasta} \\
+        --output_dir \$WORKDIR \\
+        --processes ${task.cpus} \\
+        ${args}
+
+    cat <<-END_VERSIONS > \$WORKDIR/versions.yml
+    "${task.process}":
+        varnet: 1.5.0
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p ${prefix}
+    echo "" | gzip > ${prefix}/${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        varnet: 1.0.0
+    END_VERSIONS
+    """
+}
+
diff --git a/modules/nf-core/varnet/meta.yml b/modules/nf-core/varnet/meta.yml
new file mode 100644
index 000000000000..0c9dab3ace7f
--- /dev/null
+++ b/modules/nf-core/varnet/meta.yml
@@ -0,0 +1,158 @@
+name: "varnet"
+description: DeepSomatic is an extension of deep learning-based variant caller
+  DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and
+  normal data, produces pileup image tensors from them, classifies each tensor
+  using a convolutional neural network, and finally reports somatic variants in
+  a standard VCF or gVCF file.
+keywords:
+  - variant calling
+  - machine learning
+  - neural network
+tools:
+  - "varnet":
+      description: "A deep learning based somatic variant caller"
+      homepage: "https://github.com/skandlab/varnet"
+      documentation: "https://github.com/skandlab/varnet"
+      tool_dev_url: "https://github.com/skandlab/varnet"
+      doi: "10.1038/s41467-022-30584-2"
+      licence:
+        - "Polyform Non-Commercial"
+      identifier: "biotools:deepsomatic"
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - input_normal:
+        type: file
+        description: BAM/CRAM file
+        pattern: "*.bam/cram"
+        ontologies: []
+    - index_normal:
+        type: file
+        description: Index of BAM/CRAM file
+        pattern: "*.bai/crai"
+        ontologies: []
+    - input_tumor:
+        type: file
+        description: BAM/CRAM file
+        pattern: "*.bam/cram"
+        ontologies: []
+    - index_tumor:
+        type: file
+        description: Index of BAM/CRAM file
+        pattern: "*.bai/crai"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - intervals:
+        type: file
+        description: file containing intervals
+        ontologies: []
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fasta:
+        type: file
+        description: The reference fasta file
+        pattern: "*.fasta"
+        ontologies: []
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - fai:
+        type: file
+        description: Index of reference fasta file
+        pattern: "*.fai"
+        ontologies: []
+  - - meta5:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - gzi:
+        type: file
+        description: GZI index of reference fasta file
+        pattern: "*.gzi"
+        ontologies: []
+output:
+  vcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}.vcf.gz:
+          type: file
+          description: Compressed VCF file
+          pattern: "*.vcf.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  vcf_tbi:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}.vcf.gz.tbi:
+          type: file
+          description: Index of compressed VCF file
+          pattern: "*.vcf.gz.tbi"
+          ontologies: []
+  gvcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}.g.vcf.gz:
+          type: file
+          description: Compressed GVCF file
+          pattern: "*.g.vcf.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3989
+  gvcf_tbi:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}.g.vcf.gz.tbi:
+          type: file
+          description: Index of compressed Genotyped VCF file
+          pattern: "*.g.vcf.gz.tbi"
+          ontologies: []
+  versions_deepsomatic:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - deepsomatic:
+          type: string
+          description: The name of the tool
+      - 1.7.0:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - deepsomatic:
+          type: string
+          description: The name of the tool
+      - 1.7.0:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@vaxyzek"
+maintainers:
+  - "@vaxyzek"
+
diff --git a/modules/nf-core/varnet/tests/main.nf.test b/modules/nf-core/varnet/tests/main.nf.test
new file mode 100644
index 000000000000..619b023c7bac
--- /dev/null
+++ b/modules/nf-core/varnet/tests/main.nf.test
@@ -0,0 +1,97 @@
+nextflow_process {
+
+    name "Test Process VARNET"
+    script "../main.nf"
+    process "VARNET"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "varnet"
+
+    test("tumor_normal_pair") {
+        config './nextflow.config'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
+                ]
+		input[1] = [
+    			[ id:'test_region' ],
+    			file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
+		]                
+		input[2] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        process.out.vcf.collect { file(it[1]).getName() },
+                        process.out.vcf_tbi.collect { file(it[1]).getName() },
+                        process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+test("tumor_only") {
+        config './nextflow.config'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_tumor_only' ],
+                    [], // input_normal is empty
+                    [], // index_normal is empty
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'intervals' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
+                ]
+                input[2] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                input[3] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        process.out.vcf.collect { file(it[1]).getName() },
+                        process.out.vcf_tbi.collect { file(it[1]).getName() },
+                        process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/varnet/tests/main.nf.test.snap b/modules/nf-core/varnet/tests/main.nf.test.snap
new file mode 100644
index 000000000000..81427b3cfaf2
--- /dev/null
+++ b/modules/nf-core/varnet/tests/main.nf.test.snap
@@ -0,0 +1,46 @@
+{
+    "tumor_only": {
+        "content": [
+            [
+                "test_tumor_only_out.vcf.gz"
+            ],
+            [
+                
+            ],
+            [
+                [
+                    "VARNET",
+                    "varnet",
+                    "1.0.0"
+                ]
+            ]
+        ],
+        "timestamp": "2026-05-28T17:01:27.251285842",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "tumor_normal_pair": {
+        "content": [
+            [
+                "test_out.vcf.gz"
+            ],
+            [
+                
+            ],
+            [
+                [
+                    "VARNET",
+                    "varnet",
+                    "1.0.0"
+                ]
+            ]
+        ],
+        "timestamp": "2026-05-28T16:46:04.690450597",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/varnet/tests/nextflow.config b/modules/nf-core/varnet/tests/nextflow.config
new file mode 100644
index 000000000000..632cba772ce6
--- /dev/null
+++ b/modules/nf-core/varnet/tests/nextflow.config
@@ -0,0 +1,8 @@
+process {
+    withName: VARNET {
+        ext.prefix = { "${meta.id}_out" }
+        memory = '16GB'
+        cpus   = 1
+        // ext.args is no longer needed for the region since it's handled via the input channel
+    }
+}

From 49a8dc3293e72511c449cdb3eddf611503ca2d82 Mon Sep 17 00:00:00 2001
From: kiran <kiran@GIS-SPD-FMH9B74>
Date: Fri, 29 May 2026 16:25:56 +0800
Subject: [PATCH 02/12] feat: add varnet module

---
 modules/nf-core/varnet/meta.yml | 121 +++++++++-----------------------
 1 file changed, 34 insertions(+), 87 deletions(-)

diff --git a/modules/nf-core/varnet/meta.yml b/modules/nf-core/varnet/meta.yml
index 0c9dab3ace7f..b164cfae6ea9 100644
--- a/modules/nf-core/varnet/meta.yml
+++ b/modules/nf-core/varnet/meta.yml
@@ -1,23 +1,23 @@
 name: "varnet"
-description: DeepSomatic is an extension of deep learning-based variant caller
-  DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and
-  normal data, produces pileup image tensors from them, classifies each tensor
-  using a convolutional neural network, and finally reports somatic variants in
-  a standard VCF or gVCF file.
+description: VarNet is a deep learning-based somatic variant caller that utilizes
+  a two-stage filtering and prediction architecture. It processes aligned reads from
+  tumor and normal data to identify somatic mutations using a deep neural network
+  approach.
 keywords:
   - variant calling
   - machine learning
   - neural network
+  - somatic
 tools:
   - "varnet":
-      description: "A deep learning based somatic variant caller"
-      homepage: "https://github.com/skandlab/varnet"
-      documentation: "https://github.com/skandlab/varnet"
-      tool_dev_url: "https://github.com/skandlab/varnet"
+      description: "A deep learning-based somatic variant caller"
+      homepage: "https://github.com/skandlab/VarNet"
+      documentation: "https://github.com/skandlab/VarNet"
+      tool_dev_url: "https://github.com/skandlab/VarNet"
       doi: "10.1038/s41467-022-30584-2"
       licence:
-        - "Polyform Non-Commercial"
-      identifier: "biotools:deepsomatic"
+        - "MIT"
+      identifier: ""
 input:
   - - meta:
         type: map
@@ -26,63 +26,51 @@ input:
           e.g. [ id:'test', single_end:false ]
     - input_normal:
         type: file
-        description: BAM/CRAM file
-        pattern: "*.bam/cram"
+        description: BAM/CRAM file from normal sample
+        pattern: "*.{bam,cram}"
         ontologies: []
     - index_normal:
         type: file
-        description: Index of BAM/CRAM file
-        pattern: "*.bai/crai"
+        description: Index of normal BAM/CRAM file
+        pattern: "*.{bai,crai}"
         ontologies: []
     - input_tumor:
         type: file
-        description: BAM/CRAM file
-        pattern: "*.bam/cram"
+        description: BAM/CRAM file from tumor sample
+        pattern: "*.{bam,cram}"
         ontologies: []
     - index_tumor:
         type: file
-        description: Index of BAM/CRAM file
-        pattern: "*.bai/crai"
+        description: Index of tumor BAM/CRAM file
+        pattern: "*.{bai,crai}"
         ontologies: []
   - - meta2:
         type: map
         description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          Groovy Map containing reference information
     - intervals:
         type: file
-        description: file containing intervals
+        description: BED file containing target intervals
+        pattern: "*.bed"
         ontologies: []
   - - meta3:
         type: map
         description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          Groovy Map containing reference information
     - fasta:
         type: file
         description: The reference fasta file
-        pattern: "*.fasta"
+        pattern: "*.{fasta,fa}"
         ontologies: []
   - - meta4:
         type: map
         description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          Groovy Map containing reference information
     - fai:
         type: file
         description: Index of reference fasta file
         pattern: "*.fai"
         ontologies: []
-  - - meta5:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - gzi:
-        type: file
-        description: GZI index of reference fasta file
-        pattern: "*.gzi"
-        ontologies: []
 output:
   vcf:
     - - meta:
@@ -90,69 +78,28 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - ${prefix}.vcf.gz:
-          type: file
-          description: Compressed VCF file
-          pattern: "*.vcf.gz"
-          ontologies:
-            - edam: http://edamontology.org/format_3989 # GZIP format
+      - ${prefix}/${prefix}.vcf.gz: {}
   vcf_tbi:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - ${prefix}.vcf.gz.tbi:
-          type: file
-          description: Index of compressed VCF file
-          pattern: "*.vcf.gz.tbi"
-          ontologies: []
-  gvcf:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'sample1', single_end:false ]`
-      - ${prefix}.g.vcf.gz:
-          type: file
-          description: Compressed GVCF file
-          pattern: "*.g.vcf.gz"
-          ontologies:
-            - edam: http://edamontology.org/format_3989
-  gvcf_tbi:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'sample1', single_end:false ]`
-      - ${prefix}.g.vcf.gz.tbi:
-          type: file
-          description: Index of compressed Genotyped VCF file
-          pattern: "*.g.vcf.gz.tbi"
-          ontologies: []
-  versions_deepsomatic:
-    - - ${task.process}:
-          type: string
-          description: The name of the process
-      - deepsomatic:
-          type: string
-          description: The name of the tool
-      - 1.7.0:
-          type: eval
-          description: The expression to obtain the version of the tool
+      - ${prefix}/${prefix}.vcf.gz.tbi: {}
+  versions:
+    - versions.yml: {}
 topics:
   versions:
     - - ${task.process}:
           type: string
           description: The name of the process
-      - deepsomatic:
+      - varnet:
           type: string
           description: The name of the tool
-      - 1.7.0:
-          type: eval
+      - 1.0.0:
+          type: string
           description: The expression to obtain the version of the tool
 authors:
-  - "@vaxyzek"
+  - "@kiranchari"
 maintainers:
-  - "@vaxyzek"
-
+  - "@kiranchari"

From 90a50bc8863123df0dd174fe5b109747446f1cf8 Mon Sep 17 00:00:00 2001
From: kiran <kiran@GIS-SPD-FMH9B74>
Date: Fri, 29 May 2026 16:31:34 +0800
Subject: [PATCH 03/12] feat: add varnet module

---
 modules/nf-core/varnet/meta.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/varnet/meta.yml b/modules/nf-core/varnet/meta.yml
index b164cfae6ea9..5a26005d6869 100644
--- a/modules/nf-core/varnet/meta.yml
+++ b/modules/nf-core/varnet/meta.yml
@@ -14,9 +14,9 @@ tools:
       homepage: "https://github.com/skandlab/VarNet"
       documentation: "https://github.com/skandlab/VarNet"
       tool_dev_url: "https://github.com/skandlab/VarNet"
-      doi: "10.1038/s41467-022-30584-2"
+      doi: "10.1038/s41467-022-31765-8"
       licence:
-        - "MIT"
+        - "PolyForm Noncommercial License 1.0.0"
       identifier: ""
 input:
   - - meta:

From 2b21805f43ea20e50d5f996f65c3774c66dc00ac Mon Sep 17 00:00:00 2001
From: Kiran <kirankchari@gmail.com>
Date: Wed, 3 Jun 2026 10:39:24 +0800
Subject: [PATCH 04/12] feat: add varnet module

---
 modules/nf-core/varnet/main.nf                | 15 +----
 modules/nf-core/varnet/meta.yml               | 67 +++----------------
 modules/nf-core/varnet/tests/main.nf.test     |  2 -
 .../nf-core/varnet/tests/main.nf.test.snap    | 44 ------------
 4 files changed, 13 insertions(+), 115 deletions(-)

diff --git a/modules/nf-core/varnet/main.nf b/modules/nf-core/varnet/main.nf
index dc3678510f81..737b9e487406 100644
--- a/modules/nf-core/varnet/main.nf
+++ b/modules/nf-core/varnet/main.nf
@@ -2,7 +2,6 @@ process VARNET {
     tag "$meta.id"
     label 'process_high_memory'
 
-    // Using the official VarNet Docker image
     container "docker.io/kiranchari/varnet:latest"
 
     input:
@@ -12,8 +11,8 @@ process VARNET {
     tuple val(meta4), path(fai)
 
     output:
-    tuple val(meta), path("${prefix}/${prefix}.vcf.gz")    , emit: vcf
-    tuple val("${task.process}"), val("varnet"), val("1.0.0"), emit: versions, topic: versions
+    tuple val(meta), path("${prefix}/${prefix}.vcf.gz"), emit: vcf
+    tuple val("${task.process}"), val("varnet"), val("1.5.0"), emit: versions_varnet, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -46,11 +45,6 @@ process VARNET {
         --output_dir \$WORKDIR \\
         --processes ${task.cpus} \\
         ${args}
-
-    cat <<-END_VERSIONS > \$WORKDIR/versions.yml
-    "${task.process}":
-        varnet: 1.5.0
-    END_VERSIONS
     """
 
     stub:
@@ -58,11 +52,6 @@ process VARNET {
     """
     mkdir -p ${prefix}
     echo "" | gzip > ${prefix}/${prefix}.vcf.gz
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        varnet: 1.0.0
-    END_VERSIONS
     """
 }
 
diff --git a/modules/nf-core/varnet/meta.yml b/modules/nf-core/varnet/meta.yml
index 0c9dab3ace7f..83f4ac9a9563 100644
--- a/modules/nf-core/varnet/meta.yml
+++ b/modules/nf-core/varnet/meta.yml
@@ -1,9 +1,8 @@
 name: "varnet"
-description: DeepSomatic is an extension of deep learning-based variant caller
-  DeepVariant that takes aligned reads (in BAM or CRAM format) from tumor and
-  normal data, produces pileup image tensors from them, classifies each tensor
-  using a convolutional neural network, and finally reports somatic variants in
-  a standard VCF or gVCF file.
+description: VarNet is a deep learning based somatic variant caller that takes aligned
+  reads (in BAM format) from tumor and optionally normal data, produces pileup image
+  tensors from them, classifies each tensor using a convolutional neural network, and
+  finally reports somatic variants in a VCF file.
 keywords:
   - variant calling
   - machine learning
@@ -17,7 +16,7 @@ tools:
       doi: "10.1038/s41467-022-30584-2"
       licence:
         - "Polyform Non-Commercial"
-      identifier: "biotools:deepsomatic"
+      identifier: ""
 input:
   - - meta:
         type: map
@@ -73,16 +72,6 @@ input:
         description: Index of reference fasta file
         pattern: "*.fai"
         ontologies: []
-  - - meta5:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - gzi:
-        type: file
-        description: GZI index of reference fasta file
-        pattern: "*.gzi"
-        ontologies: []
 output:
   vcf:
     - - meta:
@@ -96,48 +85,15 @@ output:
           pattern: "*.vcf.gz"
           ontologies:
             - edam: http://edamontology.org/format_3989 # GZIP format
-  vcf_tbi:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'sample1', single_end:false ]`
-      - ${prefix}.vcf.gz.tbi:
-          type: file
-          description: Index of compressed VCF file
-          pattern: "*.vcf.gz.tbi"
-          ontologies: []
-  gvcf:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'sample1', single_end:false ]`
-      - ${prefix}.g.vcf.gz:
-          type: file
-          description: Compressed GVCF file
-          pattern: "*.g.vcf.gz"
-          ontologies:
-            - edam: http://edamontology.org/format_3989
-  gvcf_tbi:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. `[ id:'sample1', single_end:false ]`
-      - ${prefix}.g.vcf.gz.tbi:
-          type: file
-          description: Index of compressed Genotyped VCF file
-          pattern: "*.g.vcf.gz.tbi"
-          ontologies: []
-  versions_deepsomatic:
+
+  versions_varnet:
     - - ${task.process}:
           type: string
           description: The name of the process
-      - deepsomatic:
+      - varnet:
           type: string
           description: The name of the tool
-      - 1.7.0:
+      - "1.5.0":
           type: eval
           description: The expression to obtain the version of the tool
 topics:
@@ -145,14 +101,13 @@ topics:
     - - ${task.process}:
           type: string
           description: The name of the process
-      - deepsomatic:
+      - varnet:
           type: string
           description: The name of the tool
-      - 1.7.0:
+      - "1.5.0":
           type: eval
           description: The expression to obtain the version of the tool
 authors:
   - "@vaxyzek"
 maintainers:
   - "@vaxyzek"
-
diff --git a/modules/nf-core/varnet/tests/main.nf.test b/modules/nf-core/varnet/tests/main.nf.test
index 619b023c7bac..5d5a8e3bcaf5 100644
--- a/modules/nf-core/varnet/tests/main.nf.test
+++ b/modules/nf-core/varnet/tests/main.nf.test
@@ -43,7 +43,6 @@ nextflow_process {
                 {
                     assert snapshot(
                         process.out.vcf.collect { file(it[1]).getName() },
-                        process.out.vcf_tbi.collect { file(it[1]).getName() },
                         process.out.versions
                     ).match()
                 }
@@ -87,7 +86,6 @@ test("tumor_only") {
                 {
                     assert snapshot(
                         process.out.vcf.collect { file(it[1]).getName() },
-                        process.out.vcf_tbi.collect { file(it[1]).getName() },
                         process.out.versions
                     ).match()
                 }
diff --git a/modules/nf-core/varnet/tests/main.nf.test.snap b/modules/nf-core/varnet/tests/main.nf.test.snap
index 81427b3cfaf2..7a73a41bfdf7 100644
--- a/modules/nf-core/varnet/tests/main.nf.test.snap
+++ b/modules/nf-core/varnet/tests/main.nf.test.snap
@@ -1,46 +1,2 @@
 {
-    "tumor_only": {
-        "content": [
-            [
-                "test_tumor_only_out.vcf.gz"
-            ],
-            [
-                
-            ],
-            [
-                [
-                    "VARNET",
-                    "varnet",
-                    "1.0.0"
-                ]
-            ]
-        ],
-        "timestamp": "2026-05-28T17:01:27.251285842",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "26.04.0"
-        }
-    },
-    "tumor_normal_pair": {
-        "content": [
-            [
-                "test_out.vcf.gz"
-            ],
-            [
-                
-            ],
-            [
-                [
-                    "VARNET",
-                    "varnet",
-                    "1.0.0"
-                ]
-            ]
-        ],
-        "timestamp": "2026-05-28T16:46:04.690450597",
-        "meta": {
-            "nf-test": "0.9.5",
-            "nextflow": "26.04.0"
-        }
-    }
 }
\ No newline at end of file

From 13ff223bc1d7b0dbefdf4b5364d3d4cebd516155 Mon Sep 17 00:00:00 2001
From: kiran <kiran@GIS-SPD-FMH9B74>
Date: Wed, 3 Jun 2026 16:47:56 +0800
Subject: [PATCH 05/12] feat: add varnet module

---
 .../nf-core/varnet/tests/main.nf.test.snap    | 26 +++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/modules/nf-core/varnet/tests/main.nf.test.snap b/modules/nf-core/varnet/tests/main.nf.test.snap
index 7a73a41bfdf7..21b5d279bc19 100644
--- a/modules/nf-core/varnet/tests/main.nf.test.snap
+++ b/modules/nf-core/varnet/tests/main.nf.test.snap
@@ -1,2 +1,28 @@
 {
+    "tumor_only": {
+        "content": [
+            [
+                "test_tumor_only_out.vcf.gz"
+            ],
+            null
+        ],
+        "timestamp": "2026-06-03T16:15:06.084936823",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
+    },
+    "tumor_normal_pair": {
+        "content": [
+            [
+                "test_out.vcf.gz"
+            ],
+            null
+        ],
+        "timestamp": "2026-06-03T16:06:07.792304371",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
+    }
 }
\ No newline at end of file

From c254f8ee0c7045e70d15f1854b276ae6adfd17fd Mon Sep 17 00:00:00 2001
From: Kiran Krishnamachari <kirankchari@gmail.com>
Date: Wed, 3 Jun 2026 20:11:14 +0800
Subject: [PATCH 06/12] Update modules/nf-core/varnet/tests/main.nf.test

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
---
 modules/nf-core/varnet/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/varnet/tests/main.nf.test b/modules/nf-core/varnet/tests/main.nf.test
index 5d5a8e3bcaf5..f9a55b16b44c 100644
--- a/modules/nf-core/varnet/tests/main.nf.test
+++ b/modules/nf-core/varnet/tests/main.nf.test
@@ -43,7 +43,7 @@ nextflow_process {
                 {
                     assert snapshot(
                         process.out.vcf.collect { file(it[1]).getName() },
-                        process.out.versions
+                        process.out.findAll { key, val -> key.startsWith('versions') }
                     ).match()
                 }
             )

From 25f5d0f0bb8ab2654f12f66acbefc1acdde75228 Mon Sep 17 00:00:00 2001
From: Kiran Krishnamachari <kirankchari@gmail.com>
Date: Wed, 3 Jun 2026 20:11:31 +0800
Subject: [PATCH 07/12] Update modules/nf-core/varnet/tests/main.nf.test

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
---
 modules/nf-core/varnet/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/varnet/tests/main.nf.test b/modules/nf-core/varnet/tests/main.nf.test
index f9a55b16b44c..ee9cca973cb6 100644
--- a/modules/nf-core/varnet/tests/main.nf.test
+++ b/modules/nf-core/varnet/tests/main.nf.test
@@ -86,7 +86,7 @@ test("tumor_only") {
                 {
                     assert snapshot(
                         process.out.vcf.collect { file(it[1]).getName() },
-                        process.out.versions
+                        process.out.findAll { key, val -> key.startsWith('versions') }
                     ).match()
                 }
             )

From 148ee0510b3f056cd2802d0c45ad7e17e7188f71 Mon Sep 17 00:00:00 2001
From: Kiran Krishnamachari <kirankchari@gmail.com>
Date: Wed, 3 Jun 2026 20:11:54 +0800
Subject: [PATCH 08/12] Update modules/nf-core/varnet/tests/nextflow.config

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
---
 modules/nf-core/varnet/tests/nextflow.config | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/modules/nf-core/varnet/tests/nextflow.config b/modules/nf-core/varnet/tests/nextflow.config
index 632cba772ce6..47ac6e1f77fb 100644
--- a/modules/nf-core/varnet/tests/nextflow.config
+++ b/modules/nf-core/varnet/tests/nextflow.config
@@ -1,8 +1,5 @@
 process {
     withName: VARNET {
         ext.prefix = { "${meta.id}_out" }
-        memory = '16GB'
-        cpus   = 1
-        // ext.args is no longer needed for the region since it's handled via the input channel
     }
 }

From 17c3b97b4b08b46f10be1f42262c31aa18ee53a1 Mon Sep 17 00:00:00 2001
From: Kiran Krishnamachari <kirankchari@gmail.com>
Date: Wed, 3 Jun 2026 20:12:06 +0800
Subject: [PATCH 09/12] Update modules/nf-core/varnet/main.nf

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
---
 modules/nf-core/varnet/main.nf | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/varnet/main.nf b/modules/nf-core/varnet/main.nf
index 737b9e487406..ed988f5f0128 100644
--- a/modules/nf-core/varnet/main.nf
+++ b/modules/nf-core/varnet/main.nf
@@ -5,10 +5,8 @@ process VARNET {
     container "docker.io/kiranchari/varnet:latest"
 
     input:
-    tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor)
-    tuple val(meta2), path(intervals)
-    tuple val(meta3), path(fasta)
-    tuple val(meta4), path(fai)
+    tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor), path(intervals)
+    tuple val(meta2), path(fasta), path(fai)
 
     output:
     tuple val(meta), path("${prefix}/${prefix}.vcf.gz"), emit: vcf

From 778e19862fb92ed8d30647d9aaf374371d872222 Mon Sep 17 00:00:00 2001
From: Kiran <kirankchari@gmail.com>
Date: Thu, 4 Jun 2026 11:54:38 +0800
Subject: [PATCH 10/12] feat: add varnet module

---
 modules/nf-core/varnet/main.nf | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/varnet/main.nf b/modules/nf-core/varnet/main.nf
index 737b9e487406..b6c6f3621ff6 100644
--- a/modules/nf-core/varnet/main.nf
+++ b/modules/nf-core/varnet/main.nf
@@ -5,14 +5,14 @@ process VARNET {
     container "docker.io/kiranchari/varnet:latest"
 
     input:
-    tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor)
+    tuple val(meta), path(input_tumor), path(index_tumor), path(input_normal), path(index_normal)
     tuple val(meta2), path(intervals)
     tuple val(meta3), path(fasta)
     tuple val(meta4), path(fai)
 
     output:
     tuple val(meta), path("${prefix}/${prefix}.vcf.gz"), emit: vcf
-    tuple val("${task.process}"), val("varnet"), val("1.5.0"), emit: versions_varnet, topic: versions
+    tuple val("${task.process}"), val("varnet"), env(VARNET_VERSION), emit: versions_varnet, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,6 +27,7 @@ process VARNET {
     WORKDIR=\$(pwd)
 
     cd /VarNet
+    export VARNET_VERSION=\$(python -c "from snvs.constants import __VERSION__; print(__VERSION__)")
     TF_CPP_MIN_LOG_LEVEL=3 python /VarNet/filter.py \\
         --sample_name ${prefix} \\
         ${normal} \\
@@ -50,6 +51,7 @@ process VARNET {
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
     """
+    export VARNET_VERSION=\$(python -c "from snvs.constants import __VERSION__; print(__VERSION__)")
     mkdir -p ${prefix}
     echo "" | gzip > ${prefix}/${prefix}.vcf.gz
     """

From 540c5bb5d9b60214885faa31071180571ac50ab2 Mon Sep 17 00:00:00 2001
From: kiran <kiran@GIS-SPD-FMH9B74>
Date: Thu, 4 Jun 2026 14:14:11 +0800
Subject: [PATCH 11/12] feat: add varnet module

---
 modules/nf-core/varnet/main.nf                |  2 +-
 modules/nf-core/varnet/tests/main.nf.test     | 13 +++++-----
 .../nf-core/varnet/tests/main.nf.test.snap    | 24 +++++++++++++++----
 modules/nf-core/varnet/tests/nextflow.config  |  4 ++++
 4 files changed, 32 insertions(+), 11 deletions(-)

diff --git a/modules/nf-core/varnet/main.nf b/modules/nf-core/varnet/main.nf
index b6c6f3621ff6..f89d8810dd30 100644
--- a/modules/nf-core/varnet/main.nf
+++ b/modules/nf-core/varnet/main.nf
@@ -12,7 +12,7 @@ process VARNET {
 
     output:
     tuple val(meta), path("${prefix}/${prefix}.vcf.gz"), emit: vcf
-    tuple val("${task.process}"), val("varnet"), env(VARNET_VERSION), emit: versions_varnet, topic: versions
+    tuple val("${task.process}"), val("varnet"), env("VARNET_VERSION"), emit: versions_varnet, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/varnet/tests/main.nf.test b/modules/nf-core/varnet/tests/main.nf.test
index ee9cca973cb6..dca55be44b11 100644
--- a/modules/nf-core/varnet/tests/main.nf.test
+++ b/modules/nf-core/varnet/tests/main.nf.test
@@ -16,10 +16,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
                 ]
 		input[1] = [
     			[ id:'test_region' ],
@@ -59,10 +59,10 @@ test("tumor_only") {
                 """
                 input[0] = [
                     [ id:'test_tumor_only' ],
-                    [], // input_normal is empty
-                    [], // index_normal is empty
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai', checkIfExists: true),
+                    [], // input_normal is empty
+                    []  // index_normal is empty
                 ]
                 input[1] = [
                     [ id:'intervals' ],
@@ -93,3 +93,4 @@ test("tumor_only") {
         }
     }
 }
+
diff --git a/modules/nf-core/varnet/tests/main.nf.test.snap b/modules/nf-core/varnet/tests/main.nf.test.snap
index 21b5d279bc19..4cce20042478 100644
--- a/modules/nf-core/varnet/tests/main.nf.test.snap
+++ b/modules/nf-core/varnet/tests/main.nf.test.snap
@@ -4,9 +4,17 @@
             [
                 "test_tumor_only_out.vcf.gz"
             ],
-            null
+            {
+                "versions_varnet": [
+                    [
+                        "VARNET",
+                        "varnet",
+                        "1.5.2"
+                    ]
+                ]
+            }
         ],
-        "timestamp": "2026-06-03T16:15:06.084936823",
+        "timestamp": "2026-06-04T14:01:04.66446019",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"
@@ -17,9 +25,17 @@
             [
                 "test_out.vcf.gz"
             ],
-            null
+            {
+                "versions_varnet": [
+                    [
+                        "VARNET",
+                        "varnet",
+                        "1.5.2"
+                    ]
+                ]
+            }
         ],
-        "timestamp": "2026-06-03T16:06:07.792304371",
+        "timestamp": "2026-06-04T13:53:19.433330376",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.3"
diff --git a/modules/nf-core/varnet/tests/nextflow.config b/modules/nf-core/varnet/tests/nextflow.config
index 47ac6e1f77fb..249b54ffa6a8 100644
--- a/modules/nf-core/varnet/tests/nextflow.config
+++ b/modules/nf-core/varnet/tests/nextflow.config
@@ -1,5 +1,9 @@
 process {
     withName: VARNET {
         ext.prefix = { "${meta.id}_out" }
+        memory = '16GB'
+        cpus   = 1
+        // ext.args is no longer needed for the region since it's handled via the input channel
+
     }
 }

From 019557ccc7d35cde00b5b63403f4a2a93feeb399 Mon Sep 17 00:00:00 2001
From: kiran <kiran@GIS-SPD-FMH9B74>
Date: Wed, 10 Jun 2026 14:11:06 +0800
Subject: [PATCH 12/12] feat: add varnet module

---
 modules/nf-core/varnet/tests/main.nf.test | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/nf-core/varnet/tests/main.nf.test b/modules/nf-core/varnet/tests/main.nf.test
index dca55be44b11..5d0589cb2588 100644
--- a/modules/nf-core/varnet/tests/main.nf.test
+++ b/modules/nf-core/varnet/tests/main.nf.test
@@ -7,9 +7,9 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "varnet"
+    config './nextflow.config'
 
     test("tumor_normal_pair") {
-        config './nextflow.config'
 
         when {
             process {
@@ -52,7 +52,6 @@ nextflow_process {
     }
 
 test("tumor_only") {
-        config './nextflow.config'
 
         when {
             process {