RSeQC split_bam.py module implementation

modules/nf-core/rseqc/splitbam/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:
+  - "bioconda::rseqc=5.0.4"

modules/nf-core/rseqc/splitbam/main.nf

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+process RSEQC_SPLITBAM {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/rseqc:5.0.4--pyhdfd78af_1' :
+        'biocontainers/rseqc:5.0.4--pyhdfd78af_1' }"
+
+    input:
+    tuple val(meta) , path(bam), path(bai)
+    tuple val(meta2), path(bed)
+
+    output:
+    tuple val(meta), path("*.in.bam")  , emit: in_bam
+    tuple val(meta), path("*.ex.bam")  , emit: ex_bam
+    tuple val(meta), path("*.junk.bam"), emit: junk_bam
+    tuple val("${task.process}"), val('rseqc'), eval('split_bam.py --version | sed "s/split_bam.py //"'), emit: versions_rseqc, topic: versions
+
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    split_bam.py \\
+        -i $bam \\
+        -r $bed \\
+        -o $prefix \\
+        $args
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.in.bam
+    touch ${prefix}.ex.bam
+    touch ${prefix}.junk.bam
+    """
+}

modules/nf-core/rseqc/splitbam/meta.yml

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+name: rseqc_splitbam
+description: Split BAM file based on gene list in BED format
+keywords:
+  - bam
+  - split
+  - rnaseq
+  - quality control
+tools:
+  - "rseqc":
+      description: |
+        RSeQC package provides a number of useful modules that can comprehensively evaluate
+        high throughput sequence data especially RNA-seq data.
+      homepage: "http://rseqc.sourceforge.net/"
+      documentation: "http://rseqc.sourceforge.net/"
+      tool_dev_url: "https://github.com/MonashBioinformaticsPlatform/RSeQC"
+      doi: "10.1093/bioinformatics/bts356"
+      licence: ["GPL-3.0-or-later"]
+      identifier: biotools:rseqc
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - bam:
+        type: file
+        description: Sorted BAM file
+        pattern: "*.{bam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_2572" # BAM
+    - bai:
+        type: file
+        description: BAM index file
+        pattern: "*.{bai}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3327" # BAI
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing reference information
+          e.g. `[ id:'reference' ]`
+    - bed:
+        type: file
+        description: Gene list in BED format to split the BAM by
+        pattern: "*.{bed}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3003" # BED
+
+output:
+  in_bam:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.in.bam":
+          type: file
+          description: BAM file containing reads that mapped to the gene list
+          pattern: "*.in.bam"
+          ontologies:
+            - edam: "http://edamontology.org/format_2572" # BAM
+  ex_bam:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.ex.bam":
+          type: file
+          description: BAM file containing reads that did not map to the gene list
+          pattern: "*.ex.bam"
+          ontologies:
+            - edam: "http://edamontology.org/format_2572" # BAM
+  junk_bam:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.junk.bam":
+          type: file
+          description: BAM file containing QC failed or unmapped reads
+          pattern: "*.junk.bam"
+          ontologies:
+            - edam: "http://edamontology.org/format_2572" # BAM
+  versions_rseqc:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - rseqc:
+          type: string
+          description: The tool name
+      - split_bam.py --version | sed "s/split_bam.py //":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - rseqc:
+          type: string
+          description: The tool name
+      - split_bam.py --version | sed "s/split_bam.py //":
+          type: eval
+          description: The expression to obtain the version of the tool
+authors:
+  - "@rhassaine"
+maintainers:
+  - "@rhassaine"

modules/nf-core/rseqc/splitbam/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process RSEQC_SPLITBAM"
+    script "../main.nf"
+    process "RSEQC_SPLITBAM"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "rseqc"
+    tag "rseqc/splitbam"
+
+    test("sarscov2 - [[meta] - bam - bai] - [[meta2] - bed]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'test_bed' ], // meta2 map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed12", checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [[meta] - bam - bai] - [[meta2] - bed] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true),
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
+                ])
+                input[1] = Channel.of([
+                    [ id:'test_bed' ], // meta2 map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/genome/bed/test.bed12", checkIfExists: true)
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out
+                ).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/rseqc/splitbam/tests/main.nf.test.snap

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+{
+    "sarscov2 - [[meta] - bam - bai] - [[meta2] - bed] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.in.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.ex.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junk.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    [
+                        "RSEQC_SPLITBAM",
+                        "rseqc",
+                        "5.0.4"
+                    ]
+                ],
+                "ex_bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.ex.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "in_bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.in.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "junk_bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junk.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_rseqc": [
+                    [
+                        "RSEQC_SPLITBAM",
+                        "rseqc",
+                        "5.0.4"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-10T08:52:06.92323219"
+    },
+    "sarscov2 - [[meta] - bam - bai] - [[meta2] - bed]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.in.bam:md5,1b683a36569410a655b2c2cd5312a9de"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.ex.bam:md5,de1a667ed02b677907c441792a9fd651"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junk.bam:md5,db5d68a1eef108c6bef2090beb0941bd"
+                    ]
+                ],
+                "3": [
+                    [
+                        "RSEQC_SPLITBAM",
+                        "rseqc",
+                        "5.0.4"
+                    ]
+                ],
+                "ex_bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.ex.bam:md5,de1a667ed02b677907c441792a9fd651"
+                    ]
+                ],
+                "in_bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.in.bam:md5,1b683a36569410a655b2c2cd5312a9de"
+                    ]
+                ],
+                "junk_bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.junk.bam:md5,db5d68a1eef108c6bef2090beb0941bd"
+                    ]
+                ],
+                "versions_rseqc": [
+                    [
+                        "RSEQC_SPLITBAM",
+                        "rseqc",
+                        "5.0.4"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2025-12-10T08:52:00.227785889"
+    }
+}