nf-core · fellen31 · Dec 7, 2025 · Dec 6, 2025
diff --git a/modules/nf-core/strdrop/build/environment.yml b/modules/nf-core/strdrop/build/environment.yml
@@ -0,0 +1,10 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::pip=25.3
+  - conda-forge::python=3.14.1
+  - pip:
+      - strdrop==0.3
diff --git a/modules/nf-core/strdrop/build/main.nf b/modules/nf-core/strdrop/build/main.nf
@@ -0,0 +1,34 @@
+process STRDROP_BUILD {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4f/4fc3114f6d67fadb826981d29ae67f8564ee81283184893c2db677d919b5b32d/data':
+        'community.wave.seqera.io/library/pip_strdrop:df8d5dc993ea6848' }"
+
+    input:
+    tuple val(meta), path(training_set, stageAs: 'input/*')
+
+    output:
+    tuple val(meta), path("*.json"), emit: json
+    tuple val("${task.process}"), val('strdrop'), eval("strdrop --version | sed 's/.* //g'"), topic: versions, emit: versions_strdrop
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    strdrop \\
+        build \\
+        --training-set ./input \\
+        ${prefix}.json
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.json
+    """
+}
diff --git a/modules/nf-core/strdrop/build/meta.yml b/modules/nf-core/strdrop/build/meta.yml
@@ -0,0 +1,68 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "strdrop_build"
+description: Build reference json from sequencing coverage in STR VCFs
+keywords:
+  - str
+  - vcf
+  - lrs
+tools:
+  - "strdrop":
+      description: "Flag STR coverage drops in LRS data"
+      homepage: "https://github.com/dnil/strdrop"
+      documentation: "https://github.com/dnil/strdrop/blob/main/docs/README.md"
+      tool_dev_url: "https://github.com/dnil/strdrop"
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - training_set:
+        type: file
+        description: Input VCF training set files
+        pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3016" # VCF
+          - edam: "http://edamontology.org/format_3020" # BCF
+output:
+  json:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.json":
+          type: file
+          description: Output reference json file
+          pattern: "*.json"
+          ontologies:
+            - edam: "http://edamontology.org/format_3464" # JSON
+  versions_strdrop:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - strdrop:
+          type: string
+          description: The name of the tool
+      - strdrop --version | sed 's/.* //g':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - strdrop:
+          type: string
+          description: The name of the tool
+      - strdrop --version | sed 's/.* //g':
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@fellen31"
+maintainers:
+  - "@fellen31"
diff --git a/modules/nf-core/strdrop/build/tests/main.nf.test b/modules/nf-core/strdrop/build/tests/main.nf.test
@@ -0,0 +1,101 @@
+nextflow_process {
+
+    name "Test Process STRDROP_BUILD"
+    script "../main.nf"
+    process "STRDROP_BUILD"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "strdrop"
+    tag "strdrop/build"
+    tag "samtools/faidx"
+    tag "gunzip"
+    tag "trgt/genotype"
+
+    setup {
+        run("GUNZIP"){
+            script "../../../gunzip/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id : 'chr22' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22_chr22_KI270734v1_random/sequence/genome.fa.gz', checkIfExists: true)
+                ]
+            """
+            }
+        }
+        run("SAMTOOLS_FAIDX"){
+            script "../../../samtools/faidx/main.nf"
+            process {
+                """
+                input[0] = GUNZIP.out.gunzip
+                input[1] = [[],[]]
+                input[2] = false
+                """
+            }
+        }
+        run("TRGT_GENOTYPE"){
+            script "../../../trgt/genotype/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                    'XX'
+                ]
+                input[1] = GUNZIP.out.gunzip
+                input[2] = SAMTOOLS_FAIDX.out.fai
+                input[3] = Channel.of('chr22\t18890357\t18890451\tID=TEST;MOTIFS=AT;STRUC=(AT)n')
+                            .collectFile(name : 'repeats.bed', newLine: false)
+                            .map { file -> [ [ id : 'chr22' ], file ] }
+                """
+            }
+        }
+    }
+
+    test("test") {
+        when {
+            process {
+                """
+                input[0] = TRGT_GENOTYPE.out.vcf
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
+            )
+        }
+
+    }
+
+    test("test-stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = TRGT_GENOTYPE.out.vcf
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(
+                    process.out,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/strdrop/build/tests/main.nf.test.snap b/modules/nf-core/strdrop/build/tests/main.nf.test.snap
@@ -0,0 +1,102 @@
+{
+    "test": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.json:md5,e918b92effa7c7c4696f3ae80e51d0d5"
+                    ]
+                ],
+                "1": [
+                    [
+                        "STRDROP_BUILD",
+                        "strdrop",
+                        "0.3"
+                    ]
+                ],
+                "json": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.json:md5,e918b92effa7c7c4696f3ae80e51d0d5"
+                    ]
+                ],
+                "versions_strdrop": [
+                    [
+                        "STRDROP_BUILD",
+                        "strdrop",
+                        "0.3"
+                    ]
+                ]
+            },
+            {
+                "versions_strdrop": [
+                    [
+                        "STRDROP_BUILD",
+                        "strdrop",
+                        "0.3"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-12-06T11:11:57.601817569"
+    },
+    "test-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        "STRDROP_BUILD",
+                        "strdrop",
+                        "0.3"
+                    ]
+                ],
+                "json": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_strdrop": [
+                    [
+                        "STRDROP_BUILD",
+                        "strdrop",
+                        "0.3"
+                    ]
+                ]
+            },
+            {
+                "versions_strdrop": [
+                    [
+                        "STRDROP_BUILD",
+                        "strdrop",
+                        "0.3"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-12-06T11:12:03.26800462"
+    }
+}