Add deepsomatic module scaffolding

modules/nf-core/deepsomatic/main.nf

@@ -0,0 +1,74 @@
+process DEEPSOMATIC {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "docker.io/google/deepsomatic:1.7.0"
+
+    input:
+    tuple val(meta), path(input_normal), path(index_normal)
+    tuple val(meta2), path(input_tumor), path(index_tumor)
+    tuple val(meta3), path(intervals)
+    tuple val(meta4), path(fasta)
+    tuple val(meta5), path(fai)
+    tuple val(meta6), path(gzi)
+
+    output:
+    tuple val(meta), path("${prefix}.vcf.gz")      ,  emit: vcf
+    tuple val(meta), path("${prefix}.vcf.gz.tbi")  ,  emit: vcf_tbi
+    tuple val(meta), path("${prefix}.g.vcf.gz")    ,  emit: gvcf
+    tuple val(meta), path("${prefix}.g.vcf.gz.tbi"),  emit: gvcf_tbi
+    path "versions.yml"                            ,  emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "DEEPSOMATIC module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def regions = intervals ? "--regions=${intervals}" : ""
+    def VERSION = '1.7.0'
+
+    """
+    run_deepsomatic \\
+        --ref=${fasta} \\
+        --reads_normal=${input_normal} \\
+        --reads_tumor=${input_tumor} \\
+        --output_vcf=${prefix}.vcf.gz \\
+        --output_gvcf=${prefix}.g.vcf.gz \\
+        --sample_name_tumor="tumor" \\
+        --sample_name_normal="normal" \\
+        ${args} \\
+        ${regions} \\
+        --intermediate_results_dir=tmp \\
+        --num_shards=${task.cpus}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deepsomatic: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "DEEPSOMATIC module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    prefix = task.ext.prefix ?: "${meta.id}"
+
+    def VERSION = '1.7.0'
+    """
+    touch ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
+    touch ${prefix}.g.vcf.gz
+    touch ${prefix}.g.vcf.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        deepsomatic: $VERSION
+    END_VERSIONS
+    """
+}

modules/nf-core/deepsomatic/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "deepsomatic"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - variant calling
+  - machine learning
+  - neural network
+tools:
+  - "deepsomatic":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: ""
+      homepage: "https://github.com/google/deepsomatic"
+      documentation: "https://github.com/google/deepsomatic"
+      tool_dev_url: "https://github.com/google/deepsomatic"
+      doi: "10.1101/2024.08.16.608331"
+      licence: ["BSD-3-clause"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - input_normal:
+      type: file
+      description: BAM/CRAM file
+      pattern: "*.bam/cram"
+  - index_normal:
+      type: file
+      description: Index of BAM/CRAM file
+      pattern: "*.bai/crai"
+  - input_tumor:
+      type: file
+      description: BAM/CRAM file
+      pattern: "*.bam/cram"
+  - index_tumor:
+      type: file
+      description: Index of BAM/CRAM file
+      pattern: "*.bai/crai"
+  - intervals:
+      type: file
+      description: Interval file for targeted regions
+      pattern: "*.bed"
+
+  ## TODO nf-core: Delete / customise this example input
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+## TODO nf-core: Add a description of all of the variables used as output
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  ## TODO nf-core: Delete / customise this example output
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+authors:
+  - "@vaxyzek"
+maintainers:
+  - "@vaxyzek"

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

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+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test deepsomatic
+nextflow_process {
+
+    name "Test Process DEEPSOMATIC"
+    script "../main.nf"
+    process "DEEPSOMATIC"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "deepsomatic"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("tumor_normal_pair") {
+
+        // TODO nf-core: If you are created a test for a chained module
+        // (the module requires running more than one process to generate the required output)
+        // add the 'setup' method here.
+        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'normal' ],
+                    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:'tumor'],
+                    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[2] = [
+                    [ id:'intervals' ],
+                    []
+                ]
+                input[3] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true)
+                ]
+                input[4] = [
+                    [ id:'genome' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true)
+                ]
+                input[5] = [
+                    [ id: 'gzi' ],
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                {
+                    assert snapshot(
+                        process.out.vcf.collect { file(it[1]).getName() },
+                        process.out.tbi.collect { file(it[1]).getName() },
+                        process.out.stats,
+                        process.out.f1r2,
+                        process.out.versions,
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+}

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

@@ -0,0 +1,68 @@
+{
+    "sarscov2 - bam - stub": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "bam": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-08-21T17:53:00.524660985"
+    },
+    "sarscov2 - bam": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "bam": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-08-21T17:52:54.704070521"
+    },
+    "tumor_normal_pair": {
+        "content": [
+            [
+
+            ],
+            [
+
+            ],
+            null,
+            null,
+            [
+
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-09-25T20:48:33.535517722"
+    }
+}

modules/nf-core/deepsomatic/tests/tags.yml

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+deepsomatic:
+  - "modules/nf-core/deepsomatic/**"