new module: fusioncatcher/fusioncatcher

modules/nf-core/fusioncatcher/fusioncatcher/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::fusioncatcher=1.33"

modules/nf-core/fusioncatcher/fusioncatcher/main.nf

@@ -0,0 +1,65 @@
+process FUSIONCATCHER_FUSIONCATCHER {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fusioncatcher:1.33--hdfd78af_5':
+        'biocontainers/fusioncatcher:1.33--hdfd78af_5' }"
+
+    input:
+    tuple val(meta), path(fastqs)
+    tuple val(meta2), path(reference)
+
+    output:
+    tuple val(meta), path("*.fusion-genes.txt"), emit: fusions, optional: true
+    tuple val(meta), path("*.summary.txt")     , emit: summary, optional: true
+    tuple val(meta), path("*.log")             , emit: log
+    path "versions.yml"                        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def input = fastqs.join(",")
+
+    def avail_mem = 3072
+    if (!task.memory) {
+        log.info '[FusionCatcher] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = (task.memory.mega*0.8).intValue()
+    }
+    """
+    fusioncatcher \\
+        --input=${input} \\
+        --output=. \\
+        --data=${reference} \\
+        --threads=${task.cpus} \\
+        --Xmx=${avail_mem} \\
+        ${args}
+
+    mv final-list_candidate-fusion-genes.txt ${prefix}.fusion-genes.txt
+    mv summary_candidate_fusions.txt ${prefix}.summary.txt
+    mv fusioncatcher.log ${prefix}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fusioncatcher: "\$(fusioncatcher --version 2>&1 | awk '{print \$2}')"
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.fusion-genes.txt
+    touch ${prefix}.summary.txt
+    touch ${prefix}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fusioncatcher: "\$(fusioncatcher --version 2>&1 | awk '{print \$2}')"
+    END_VERSIONS
+    """
+}

modules/nf-core/fusioncatcher/fusioncatcher/meta.yml

@@ -0,0 +1,78 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "fusioncatcher_fusioncatcher"
+description: FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data
+keywords:
+  - fusion
+  - rna
+  - fastq
+tools:
+  - fusioncatcher:
+      description: FusionCatcher searches for novel/known somatic fusion genes, translocations, and chimeras in RNA-seq data
+      homepage: https://github.com/ndaniel/fusioncatcher
+      documentation: https://github.com/ndaniel/fusioncatcher/wiki
+      tool_dev_url: https://github.com/ndaniel/fusioncatcher
+      doi: "10.1101/011650v1"
+      licence: ["GPL v3"]
+      identifier: biotools:fusioncatcher
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - fastqs:
+        type: list
+        description: A list of input fastq files
+        pattern: "*.{fastq,fq}.gz"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - reference:
+        type: file
+        description: Directory containing fusioncatcher reference files
+
+output:
+  - fusions:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - "*.fusion-genes.txt":
+        type: file
+        description: The detected fusions in the input files
+        pattern: "*.fusion-genes.txt"
+  - summary:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - "*.summary.txt":
+        type: file
+        description: The generated summary
+        pattern: "*.summary.txt"
+  - log:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - "*.log":
+        type: file
+        description: The Fusioncatcher log
+        pattern: "*.log"
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@nvnieuwk"
+maintainers:
+  - "@nvnieuwk"

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

@@ -0,0 +1,43 @@
+nextflow_process {
+
+    name "Test Process FUSIONCATCHER_FUSIONCATCHER"
+    script "../main.nf"
+    process "FUSIONCATCHER_FUSIONCATCHER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fusioncatcher"
+    tag "fusioncatcher/fusioncatcher"
+
+    // Only stub tests because the refernce is about 50 GB of data
+
+    test("sarscov2 - fastq - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
+                ]
+                input[1] = [
+                    [ id:'reference'],
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

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

@@ -0,0 +1,73 @@
+{
+    "sarscov2 - fastq - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fusion-genes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,6a54daab2ec7621d8493678e832cf45e"
+                ],
+                "fusions": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fusion-genes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "log": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "summary": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6a54daab2ec7621d8493678e832cf45e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-04-11T11:01:13.392512529"
+    }
+}