pypgx/runngspipeline

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

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+process PYPGX_RUNNGSPIPELINE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pypgx:0.25.0--pyh7e72e81_0':
+        'biocontainers/pypgx:0.25.0--pyh7e72e81_0' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi), path(coverage), path(control_stats), val(pgx_gene)
+    tuple val(meta2), path(resource_bundle)
+    val(assembly_version)
+
+    output:
+    tuple val(meta), path("*pypgx_output/results.zip"), emit: results
+    tuple val(meta), path("*pypgx_output/cnv-calls.zip"), emit: cnv_calls, optional: true
+    tuple val(meta), path("*pypgx_output/consolidated-variants.zip"), emit: consolidated_variants
+    path("versions.yml"), emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}_${pgx_gene}"
+    def assembly = assembly_version ?: "GRCh38"
+    def depth_coverage = coverage ? "--depth-of-coverage ${coverage}" : ""
+    def control_statistics = control_stats ? "--control-statistics ${control_stats}" : ""
+
+    """
+    export MPLCONFIGDIR="/tmp/"
+    export PYPGX_BUNDLE=${resource_bundle}/
+
+    pypgx run-ngs-pipeline \\
+        --assembly ${assembly} \\
+        ${pgx_gene} \\
+        ${prefix}_pypgx_output/ \\
+        --variants ${vcf} \\
+        ${depth_coverage} \\
+        ${control_statistics}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pypgx: \$(echo \$(pypgx -v 2>&1) | sed 's/.* //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}_${pgx_gene}"
+
+    """
+    mkdir ${prefix}_pypgx_output
+    # zip program unavailable in container
+    python -c 'import zipfile; zipfile.ZipFile("${prefix}_pypgx_output/results.zip", "w").close()'
+    python -c 'import zipfile; zipfile.ZipFile("${prefix}_pypgx_output/cnv-calls.zip", "w").close()'
+    python -c 'import zipfile; zipfile.ZipFile("${prefix}_pypgx_output/consolidated-variants.zip", "w").close()'
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pypgx: \$(echo \$(pypgx -v 2>&1) | sed 's/.* //')
+    END_VERSIONS
+    """
+}

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

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "pypgx_runngspipeline"
+
+description: PyPGx pharmacogenomics genotyping pipeline for NGS data.
+keywords:
+  - pypgx
+  - pharmacogenetics
+  - genotyping
+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 ]`.
+    - vcf:
+        type: file
+        description: BGZIP compressed VCF file with SNVs/indels. Output of pypgx/createinputvcf.
+        pattern: "*.{vcf.gz}"
+    - tbi:
+        type: file
+        description: VCF tabix index.
+        pattern: "*.{vcf.gz.tbi}"
+    - coverage:
+        type: file
+        description: ZIP compressed file with depth of coverage information. Output
+          of pypgx/preparedepthofcoverage. Coverage information is only required when
+          running the module on a pharmacogene with known structural variants.
+        pattern: "*.{zip}"
+    - control_stats:
+        type: file
+        description: ZIP compressed file with control statistics. Output of pypgx/computecontrolstatistics.
+          Control statistics are only required when running the module on a pharmacogene
+          with known structural variants.
+    - pgx_gene:
+        type: string
+        description: Pharmacogene to genotype/phenotype. A list of supported genes is
+          available in the pypgx documentation "https://pypgx.readthedocs.io/en/latest/genes.html"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`.
+    - resource_bundle:
+        type: directory
+        description: Path to the pypgx resource bundle (https://github.com/sbslee/pypgx-bundle).
+  - - assembly_version:
+        type: string
+        description: Genome assembly version to use.
+output:
+  - results:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*pypgx_output/results.zip":
+          type: file
+          description: Main output file of the pipeline in ZIP format, containing a table
+            with star-alleles per sample and CNV calls where applicable.
+  - cnv_calls:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*pypgx_output/cnv-calls.zip":
+          type: file
+          description: Optional output file in ZIP format, containing CNV calls per sample.
+  - consolidated_variants:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*pypgx_output/consolidated-variants.zip":
+          type: file
+          description: Output file in ZIP format, containing a consolidated (and phased)
+            VCF file.
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@jorivansteenbrugge"
+maintainers:
+  - "@jorivansteenbrugge"

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

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+nextflow_process {
+
+    name "Test Process PYPGX_RUNNGSPIPELINE"
+    script "../main.nf"
+    process "PYPGX_RUNNGSPIPELINE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pypgx"
+    tag "pypgx/runngspipeline"
+    tag "pypgx/createinputvcf"
+    tag "pypgx/computecontrolstatistics"
+    tag "pypgx/preparedepthofcoverage"
+    tag "untar"
+
+    test("human paired end bam - CYP2D6 locus - GRCh37 - CYP2D6 pharmacogene") {
+        setup {
+            run("PYPGX_CREATEINPUTVCF") {
+                script "../../createinputvcf/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [id: 'test'], // meta map
+                        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] = [
+                        [id: 'GRCh37'], // meta2 map
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/GRCh37_chr22.fasta.gz', checkIfExists: true)
+                    ]
+                    input[2] = ["CYP2D6"] // Pharmacogene
+                    input[3] = "GRCh37" // assembly version
+                    """
+                }
+            }
+            run("PYPGX_PREPAREDEPTHOFCOVERAGE") {
+                script "../../preparedepthofcoverage"
+                process {
+                    """
+                    input[0] = [
+                        [id: 'test'], // meta map
+                        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"] // Pharmacogene
+                    input[2] = "GRCh37" // assembly version
+                    """
+                }
+            }
+            run("PYPGX_COMPUTECONTROLSTATISTICS") {
+                script "../../computecontrolstatistics/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [id: 'test'], // meta map
+                        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] = "22:42512500-42551883"
+                    input[2] = "GRCh37" // assembly version
+                    """
+                }
+            }
+            run("UNTAR") {
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [id: 'resource_bundle'],
+                        file('https://github.com/sbslee/pypgx-bundle/archive/refs/tags/0.25.0.tar.gz')
+                    ]
+                    """
+                }
+            }
+        }
+        when {
+            process {
+                """
+                input[0] = PYPGX_CREATEINPUTVCF.out.vcf
+                            .join(PYPGX_CREATEINPUTVCF.out.tbi)
+                            .join(PYPGX_PREPAREDEPTHOFCOVERAGE.out.coverage)
+                            .join(PYPGX_COMPUTECONTROLSTATISTICS.out.control_stats)
+                            .combine(Channel.fromList(["CYP2D6"]))
+                input[1] = UNTAR.out.untar // resource bundle
+                input[2] = 'GRCh37' //assembly version
+                """
+            }
+        }
+
+        then {
+            def results = process.out.results[0][1]
+
+
+            def zipFile = path(results).zip
+            def paths = zipFile.extractAll()
+            def metaFile = paths.find { it.getFileName().toString() == 'metadata.txt' }
+
+            assertAll(
+                { assert process.success },
+                { assert zipFile.isValid() },
+                { assert paths.size() == 2 },
+                { assert snapshot(
+                    metaFile,
+                    process.out.versions).match()}
+            )
+        }
+    }
+
+    test("stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [[id: 'test'], [], [], [], [], 'gene']
+                input[1] = [[id: 'bundle'], []]
+                input[2] = ''
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

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

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+{
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "results.zip:md5,76cdb2bad9582d23c1f6f4d868218d6c"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "cnv-calls.zip:md5,76cdb2bad9582d23c1f6f4d868218d6c"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "consolidated-variants.zip:md5,76cdb2bad9582d23c1f6f4d868218d6c"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,9eab385d76a79cf80f7ca26a25592525"
+                ],
+                "cnv_calls": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "cnv-calls.zip:md5,76cdb2bad9582d23c1f6f4d868218d6c"
+                    ]
+                ],
+                "consolidated_variants": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "consolidated-variants.zip:md5,76cdb2bad9582d23c1f6f4d868218d6c"
+                    ]
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "results.zip:md5,76cdb2bad9582d23c1f6f4d868218d6c"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9eab385d76a79cf80f7ca26a25592525"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2025-01-10T10:50:49.324358"
+    },
+    "human paired end bam - CYP2D6 locus - GRCh37 - CYP2D6 pharmacogene": {
+        "content": [
+            "metadata.txt:md5,ea596a886920435c2a3c719b0ae85a8a",
+            [
+                "versions.yml:md5,9eab385d76a79cf80f7ca26a25592525"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2025-01-10T13:48:55.071007"
+    }
+}