Add varnet (https://github.com/skandlab/VarNet)

modules/nf-core/varnet/main.nf

@@ -0,0 +1,57 @@
+process VARNET {
+    tag "$meta.id"
+    label 'process_high_memory'
+
+    container "docker.io/kiranchari/varnet:latest"
+
+    input:
+    tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor)
+    tuple val(meta2), path(intervals)
+    tuple val(meta3), path(fasta)
+    tuple val(meta4), path(fai)
+
+    output:
+    tuple val(meta), path("${prefix}/${prefix}.vcf.gz"), emit: vcf
+    tuple val("${task.process}"), val("varnet"), val("1.5.0"), emit: versions_varnet, 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} \\
+        ${args}
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir -p ${prefix}
+    echo "" | gzip > ${prefix}/${prefix}.vcf.gz
+    """
+}
+

modules/nf-core/varnet/meta.yml

@@ -0,0 +1,112 @@
+name: "varnet"
+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"
+      doi: "10.1038/s41467-022-31765-8"
+      licence:
+        - "PolyForm Noncommercial License 1.0.0"
+      identifier: ""
+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 from normal sample
+        pattern: "*.{bam,cram}"
+        ontologies: []
+    - index_normal:
+        type: file
+        description: Index of normal BAM/CRAM file
+        pattern: "*.{bai,crai}"
+        ontologies: []
+    - input_tumor:
+        type: file
+        description: BAM/CRAM file from tumor sample
+        pattern: "*.{bam,cram}"
+        ontologies: []
+    - index_tumor:
+        type: file
+        description: Index of tumor BAM/CRAM file
+        pattern: "*.{bai,crai}"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+    - intervals:
+        type: file
+        description: BED file containing target intervals
+        pattern: "*.bed"
+        ontologies: []
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing reference information
+    - fasta:
+        type: file
+        description: The reference fasta file
+        pattern: "*.{fasta,fa}"
+        ontologies: []
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing reference information
+    - fai:
+        type: file
+        description: Index of reference fasta file
+        pattern: "*.fai"
+        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
+
+  versions_varnet:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - varnet:
+          type: string
+          description: The name of the tool
+      - "1.5.0":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - varnet:
+          type: string
+          description: The name of the tool
+      - "1.5.0":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@kiranchari"
+maintainers:
+  - "@kiranchari"

modules/nf-core/varnet/tests/main.nf.test

@@ -0,0 +1,95 @@
+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.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.versions
+                    ).match()
+                }
+            )
+        }
+    }
+}

modules/nf-core/varnet/tests/main.nf.test.snap

@@ -0,0 +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"
+        }
+    }
+}

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
+    }
+}