Pypgx/preparedepthofcoverage

modules/nf-core/pypgx/preparedepthofcoverage/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::pypgx=0.25.0"

modules/nf-core/pypgx/preparedepthofcoverage/main.nf

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+process PYPGX_PREPAREDEPTHOFCOVERAGE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pypgx:0.25.0--pyh7e72e81_0':
+        'biocontainers/pypgx:0.25.0--pyh7e72e81_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    val(pgx_genes)
+    val(assembly_version)
+
+    output:
+    tuple val(meta), path('*.zip'), emit: coverage
+    path("versions.yml"), emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def genes = "--genes ${pgx_genes.join(' ')}" ?: ''
+    def assembly = assembly_version ?: "GRCh38"
+
+    """
+    pypgx prepare-depth-of-coverage \\
+        ${args} \\
+        ${genes} \\
+        --assembly ${assembly} \\
+        ${prefix}.zip \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pypgx: \$(echo \$(pypgx -v 2>&1) | sed 's/.* //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    python -c 'import zipfile; zipfile.ZipFile("${prefix}.zip", "w").close()'
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pypgx: \$(echo \$(pypgx -v 2>&1) | sed 's/.* //')
+    END_VERSIONS
+    """
+}

modules/nf-core/pypgx/preparedepthofcoverage/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "pypgx_preparedepthofcoverage"
+description: Prepare a depth of coverage file for all target genes with SV from BAM
+  files.
+keywords:
+  - Pharmacogenetics
+  - pypgx
+  - SV
+tools:
+  - "pypgx":
+      description: "A Python package for pharmacogenomics research"
+      homepage: "https://pypgx.readthedocs.io/en/latest/"
+      documentation: "https://pypgx.readthedocs.io/en/latest/"
+      tool_dev_url: "https://github.com/sbslee/pypgx"
+      doi: "10.1371/journal.pone.0272129"
+      licence: ["MIT"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - bam:
+        type: file
+        description: Input BAM file
+        pattern: "*.{bam}"
+    - bai:
+        type: file
+        description: Input BAM index file
+        pattern: "*.{bam.bai}"
+  - - pgx_genes:
+        type: list
+        description: List of PGx genes supported by PyPGx to include in variant calling.
+  - - assembly_version:
+        type: string
+        description: Genome assembly version to use.
+        pattern: "{GRCh37,GRCh38}"
+output:
+  - coverage:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+          pattern: "*.{zip}"
+      - "*.zip":
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+          pattern: "*.{zip}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@jorivansteenbrugge"
+maintainers:
+  - "@jorivansteenbrugge"

modules/nf-core/pypgx/preparedepthofcoverage/tests/main.nf.test

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+// nf-core modules test pypgx/preparedepthofcoverage
+nextflow_process {
+
+    name "Test Process PYPGX_PREPAREDEPTHOFCOVERAGE"
+    script "../main.nf"
+    process "PYPGX_PREPAREDEPTHOFCOVERAGE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pypgx"
+    tag "pypgx/preparedepthofcoverage"
+
+    test("human paired end bam CYP2D6 locus - GRCh37") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.PGx.CYP2D6.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.PGx.CYP2D6.bam.bai', checkIfExists: true)
+                ]
+                input[1] = ["CYP2D6"]
+                input[2] = "GRCh37"
+                """
+            }
+        }
+        then {
+            def zipFile = path(process.out.coverage[0][1]).zip
+            def paths = zipFile.extractAll()
+            def metaFile = paths.find { it.getFileName().toString() == 'metadata.txt' }
+            def dataFile = paths.find { it.getFileName().toString() == 'data.tsv' }
+
+            assertAll(
+                {assert process.success},
+                {assert zipFile.isValid()},
+                {assert snapshot(
+                    metaFile,
+                   dataFile).match()}
+            )
+        }
+    }
+
+    test("stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    [],
+                    []
+                ]
+                input[1] = []
+                input[2] = ""
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/pypgx/preparedepthofcoverage/tests/main.nf.test.snap

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+{
+    "human paired end bam CYP2D6 locus - GRCh37": {
+        "content": [
+            "metadata.txt:md5,36e844724abd194e915ca0a9793cddc8",
+            "data.tsv:md5,4291d10aa774208ba97a9b753face059"
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-10-04T08:27:28.096562"
+    },
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.zip:md5,76cdb2bad9582d23c1f6f4d868218d6c"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,245a2588c91875e1fe561955c4a0ad27"
+                ],
+                "coverage": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.zip:md5,76cdb2bad9582d23c1f6f4d868218d6c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,245a2588c91875e1fe561955c4a0ad27"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-10-04T08:27:34.813018"
+    }
+}

modules/nf-core/pypgx/preparedepthofcoverage/tests/tags.yml

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+pypgx/preparedepthofcoverage:
+  - "modules/nf-core/pypgx/preparedepthofcoverage/**"