Add paraphrase

modules/nf-core/paraphrase/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::pip==26.0.1
+  - conda-forge::python=3.14.3
+  - pip:
+      - paraphrase==0.2.0

modules/nf-core/paraphrase/main.nf

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+process PARAPHRASE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bc/bc177b8e7e1d9bbdcbb64a6ad630c7ecc63a2229ce2b219408888bc2bb34cac3/data':
+        'community.wave.seqera.io/library/pip_paraphrase:59a4576966ee5f0b' }"
+
+    input:
+    tuple val(meta), path(jsons), val(samples)
+    tuple val(meta2), path(yaml)
+    val(tsv_output)
+
+    output:
+    tuple val(meta), path("*.json"), emit: json, optional: true
+    tuple val(meta), path("*.tsv"), emit: tsv, optional: true
+
+    tuple val("${task.process}"), val('paraphrase'), eval("paraphrase --version"), topic: versions, emit: versions_paraphrase
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def rules = yaml ? "--rules $yaml" : ''
+    def output_format = tsv_output ? 'tsv' : 'json'
+    """
+    paraphrase \
+        $args \
+        --input ${jsons.join(' --input ')} \
+        --sample ${samples.join(' --sample ')} \
+        --output-format=${output_format} \
+        $rules \
+        > ${prefix}.${output_format}
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def output_format = tsv_output ? 'tsv' : 'json'
+    """
+    echo $args
+
+    touch ${prefix}.${output_format}
+    """
+}

modules/nf-core/paraphrase/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "paraphrase"
+description: Parse and annotate paraphrase JSONs
+keywords:
+  - long-read
+  - paraphrase
+  - annotate
+tools:
+  - "paraphrase":
+      description: "Paraphase JSON parser"
+      homepage: "https://github.com/Clinical-Genomics/paraphrase"
+      documentation: "https://github.com/Clinical-Genomics/paraphrase/README.md"
+      tool_dev_url: "https://github.com/Clinical-Genomics/paraphrase"
+      licence: ["MIT"]
+
+input:
+  - - meta:
+        type: map
+        description: Groovy Map containing sample information. e.g. `[ id:'sample1']`
+    - jsons:
+        type: file
+        description: "One or more JSON files from paraphase"
+        pattern: "*.json"
+        ontologies:
+          - edam: http://edamontology.org/format_3464 # JSON
+    - samples:
+        type: list
+        description: "Sample names corresponding to the JSON files. Must be in the same order as the JSON files."
+  - - meta2:
+        type: map
+        description: Groovy Map containing reference information.
+    - yaml:
+        type: file
+        description: "YAML file containing rules for annotation"
+        pattern: "*.yaml"
+        ontologies:
+          - edam: http://edamontology.org/format_3473 # YAML
+  - tsv_output:
+      type: boolean
+      description: "Whether to output in TSV format instead of JSON. Default is false (JSON output)."
+
+output:
+  json:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[ id:'sample1']`
+      - "*.json":
+          type: file
+          description: "Annotated output in JSON format"
+          pattern: "*.json"
+          ontologies:
+            - edam: http://edamontology.org/format_3464 # JSON
+  tsv:
+    - - meta:
+          type: map
+          description: Groovy Map containing sample information. e.g. `[ id:'sample1']`
+      - "*.tsv":
+          type: file
+          description: "Annotated output in TSV format"
+          pattern: "*.tsv"
+          ontologies:
+            - edam: http://edamontology.org/format_3475 # TSV
+  versions_paraphrase:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - paraphrase:
+          type: string
+          description: The name of the tool
+      - paraphrase --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - paraphrase:
+          type: string
+          description: The name of the tool
+      - paraphrase --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@fellen31"
+maintainers:
+  - "@fellen31"

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

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+nextflow_process {
+
+    name "Test Process PARAPHRASE"
+    script "../main.nf"
+    process "PARAPHRASE"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tabix/bgzip"
+    tag "paraphase"
+    tag "paraphrase"
+
+    setup {
+        run("TABIX_BGZIP") {
+            script "../../tabix/bgzip/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'test_ref' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr22_chr22_KI270734v1_random/sequence/genome.fa.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+        run("PARAPHASE") {
+            script "../../paraphase/main.nf"
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    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),
+                ]
+                input[1] = TABIX_BGZIP.out.output
+                input[2] = [
+                    [:],
+                    []
+                ]
+                """
+            }
+        }
+    }
+
+    test("no rules") {
+
+        when {
+            params {
+                module_args = '--gene PRODH'
+            }
+            process {
+                """
+                input[0] = PARAPHASE.out.json.map { meta, json -> [meta, json, meta.id] }
+                input[1] = [[],[]]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("rules") {
+
+        when {
+            params {
+                module_args = '--gene PRODH'
+            }
+            process {
+                """
+                input[0] = PARAPHASE.out.json.map { meta, json -> [meta, json, meta.id] }
+                input[1] = [
+                    [ id:'rules' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/yaml/rules.yaml', checkIfExists: true)
+                ]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("rules - tsv output") {
+
+        when {
+            params {
+                module_args = '--gene PRODH'
+            }
+            process {
+                """
+                input[0] = PARAPHASE.out.json.map { meta, json -> [meta, json, meta.id] }
+                input[1] = [
+                    [ id:'rules' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/yaml/rules.yaml', checkIfExists: true)
+                ]
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}