feat (closes #7246): add new component: leafcutter/differentialsplicing

modules/nf-core/leafcutter/differentialsplicing/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::leafcutter=2.0.3"

modules/nf-core/leafcutter/differentialsplicing/main.nf

@@ -0,0 +1,43 @@
+process LEAFCUTTER_DIFFERENTIALSPLICING {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/leafcutter:2.0.3--pyhd8ed1ab_0':
+        'quay.io/biocontainers/leafcutter:2.0.3--pyhd8ed1ab_0' }"
+
+    input:
+    tuple val(meta), path(counts), path(groups)
+
+    output:
+    tuple val(meta), path("*_cluster_significance.txt"), emit: cluster_significance
+    tuple val(meta), path("*_effect_sizes.txt")        , emit: effect_sizes
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    tuple val("${task.process}"), val('leafcutter'), val("2.0.3"), topic: versions, emit: versions_leafcutter
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    export USER="\${USER:-nobody}"
+    export PYTHONHASHSEED=0
+
+    leafcutter-ds \\
+        $counts \\
+        $groups \\
+        --output_prefix ${prefix} \\
+        --num_threads $task.cpus \\
+        $args
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_cluster_significance.txt
+    touch ${prefix}_effect_sizes.txt
+    """
+}

modules/nf-core/leafcutter/differentialsplicing/meta.yml

@@ -0,0 +1,83 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "leafcutter_differentialsplicing"
+description: Perform differential splicing analysis to identify junctions with significant changes in splicing between conditions
+keywords:
+  - alternative splicing
+  - differential splicing
+  - RNA-seq
+  - intron usage
+tools:
+  - "leafcutter":
+      description: "Annotation-free quantification of RNA splicing from RNA-seq data"
+      homepage: "https://leafcutter2.github.io/leafcutter-ds/"
+      documentation: "https://leafcutter2.github.io/leafcutter-ds/tutorials/differential-splicing/"
+      tool_dev_url: "https://github.com/leafcutter2/leafcutter-ds"
+      doi: "10.1038/s41588-017-0004-9"
+      licence: ["Apache-2.0"]
+      identifier: biotools:leafcutter
+      args_id: "$args"
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test' ]`
+    - counts:
+        type: file
+        description: Intron usage counts file from leafcutter-cluster (either perind.counts.gz or perind_numers.counts.gz)
+        pattern: "*.counts.gz"
+    - groups:
+        type: file
+        description: Tab-delimited file with sample names in column 1 and sample group/phenotype assignments in column 2
+        pattern: "*.txt"
+
+output:
+  cluster_significance:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*_cluster_significance.txt":
+          type: file
+          description: Cluster-level differential splicing statistics including p-values and test status
+          pattern: "*_cluster_significance.txt"
+  effect_sizes:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test' ]`
+      - "*_effect_sizes.txt":
+          type: file
+          description: Per-intron junction effect sizes, PSI values, and delta PSI for each condition
+          pattern: "*_effect_sizes.txt"
+  versions_leafcutter:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "leafcutter":
+          type: string
+          description: The name of the tool
+      - "2.0.3":
+          type: string
+          description: The version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - leafcutter:
+          type: string
+          description: The name of the tool
+      - "2.0.3":
+          type: string
+          description: The version of the tool
+authors:
+  - "@JTL-lab"
+maintainers:
+  - "@JTL-lab"
+notes:
+  - This module uses PyTorch for statistical analysis. Environment variables are automatically set in the module for container compatibility (`USER` defaults to 'nobody' if unset to prevent Pytorch cache initialization errors, `PYTHONHASHSEED=0` is set for reproducibility).

modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test

@@ -0,0 +1,123 @@
+nextflow_process {
+
+    name "Test Process LEAFCUTTER_DIFFERENTIALSPLICING"
+    script "../main.nf"
+    process "LEAFCUTTER_DIFFERENTIALSPLICING"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "leafcutter"
+    tag "leafcutter/differentialsplicing"
+    tag "leafcutter/clusterregtools"
+    tag "regtools"
+    tag "regtools/junctionsextract"
+
+    test("homo_sapiens - bam - differential splicing") {
+
+        config "./nextflow.config"
+
+        setup {
+            run("REGTOOLS_JUNCTIONSEXTRACT") {
+                script "../../../regtools/junctionsextract/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of(
+                        [
+                            [ id:'ctrl_rep1', single_end:false ],
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
+                        ],
+                        [
+                            [ id:'ctrl_rep2', single_end:false ],
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
+                        ],
+                        [
+                            [ id:'kd_rep1', single_end:false ],
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
+                        ],
+                        [
+                            [ id:'kd_rep2', single_end:false ],
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam", checkIfExists: true),
+                            file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.chr6.bam.bai", checkIfExists: true)
+                        ]
+                    )
+                    input[1] = ''
+                    """
+                }
+            }
+
+            run("LEAFCUTTER_CLUSTERREGTOOLS") {
+                script "../../../leafcutter/clusterregtools/main.nf"
+                process {
+                    """
+                    input[0] = REGTOOLS_JUNCTIONSEXTRACT.out.junc
+                        .map { meta, junc -> junc }
+                        .collect()
+                        .map { junc_files -> [ [ id:'test_ds' ], junc_files ] }
+                    """
+                }
+            }
+        }
+
+        when {
+            params {
+                module_args = '--min_samples_per_group 2 --min_samples_per_intron 2'
+            }
+            process {
+                """
+                def groups_content = '''ctrl_rep1\\tCONTROL
+ctrl_rep2\\tCONTROL
+kd_rep1\\tKNOCKDOWN
+kd_rep2\\tKNOCKDOWN
+'''
+                def groups_file = file("\${workDir}/groups_file.txt")
+                groups_file.text = groups_content
+
+                input[0] = LEAFCUTTER_CLUSTERREGTOOLS.out.numers
+                    .map { meta, counts -> [ meta, counts, groups_file ] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["cluster_significance", "effect_sizes"])).match()}
+            )
+        }
+
+    }
+
+    test("homo_sapiens - bam - differential splicing - stub") {
+
+        config "./nextflow.config"
+
+        options "-stub"
+
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file('test_perind.counts.gz'),
+                    file('groups_file.txt')
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/leafcutter/differentialsplicing/tests/main.nf.test.snap

@@ -0,0 +1,70 @@
+{
+    "homo_sapiens - bam - differential splicing": {
+        "content": [
+            {
+                "cluster_significance": [
+                    [
+                        {
+                            "id": "test_ds"
+                        },
+                        "test_ds_cluster_significance.txt"
+                    ]
+                ],
+                "effect_sizes": [
+                    [
+                        {
+                            "id": "test_ds"
+                        },
+                        "test_ds_effect_sizes.txt"
+                    ]
+                ],
+                "versions_leafcutter": [
+                    [
+                        "LEAFCUTTER_DIFFERENTIALSPLICING",
+                        "leafcutter",
+                        "2.0.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-28T12:22:48.849459725",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.0"
+        }
+    },
+    "homo_sapiens - bam - differential splicing - stub": {
+        "content": [
+            {
+                "cluster_significance": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_cluster_significance.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "effect_sizes": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_effect_sizes.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_leafcutter": [
+                    [
+                        "LEAFCUTTER_DIFFERENTIALSPLICING",
+                        "leafcutter",
+                        "2.0.3"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-07-28T12:00:56.961347309",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.0"
+        }
+    }
+}

modules/nf-core/leafcutter/differentialsplicing/tests/nextflow.config

@@ -0,0 +1,11 @@
+singularity {
+    pullTimeout = 30.m
+}
+
+process {
+
+    withName: 'LEAFCUTTER_DIFFERENTIALSPLICING' {
+        ext.args = { params.module_args ?: '' }
+    }
+
+}