pypgx/createinputvcf

modules/nf-core/pypgx/createinputvcf/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::pypgx=0.25.0

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

@@ -0,0 +1,56 @@
+process PYPGX_CREATEINPUTVCF {
+    tag "$meta.id"
+    label "process_single"
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/pypgx:0.25.0--pyh7e72e81_0':
+        'biocontainers/pypgx:0.25.0--pyh7e72e81_0' }"
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    tuple val(meta2), path(fasta)
+
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi
+    path("versions.yml"), emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def assembly = task.ext.assembly_version ?: "GRCh38"
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def pgx_genes = "--genes ${task.ext.pgx_genes.join(' ')}" ?: ''
+
+    """
+    pypgx create-input-vcf \\
+        ${args} \\
+        ${pgx_genes} \\
+        --assembly ${assembly} \\
+        ${prefix}_variants.vcf.gz \\
+        ${fasta} \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${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}"
+    """
+    touch ${prefix}_variants.vcf.gz
+    touch ${prefix}_variants.vcf.gz.tbi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        pypgx: \$(echo \$(pypgx -v 2>&1) | sed 's/.* //')
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,69 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "pypgx_createinputvcf"
+description: Call SNVs/indels from BAM files for all target genes.
+keywords:
+  - pypgx
+  - Pharmacogenetics
+  - variants
+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: 'test']
+    - bam:
+        type: file
+        description: Input BAM file
+        pattern: "*.{bam}"
+    - bai:
+        type: file
+        description: Input BAM index file
+        pattern: "*.{bam.bai}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [id: 'test']
+    - fasta:
+        type: file
+        description: Reference genome file
+        pattern: "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}"
+output:
+  - vcf:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [id: 'test']
+      - "*.vcf.gz":
+          type: file
+          description: VCF file containing called SNVs/indels
+          pattern: "*.vcf.gz"
+  - tbi:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [id: 'test']
+      - "*.vcf.gz.tbi":
+          type: file
+          description: File containing the VCF tabix index
+          pattern: "*.vcf.gz.tbi"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@jorisvansteenbrugge"
+maintainers:
+  - "@jorisvansteenbrugge"

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

@@ -0,0 +1,71 @@
+// nf-core modules test pypgx/createinputvcf
+nextflow_process {
+
+    name "Test Process PYPGX_CREATEINPUTVCF"
+    script "../main.nf"
+    process "PYPGX_CREATEINPUTVCF"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "pypgx"
+    tag "pypgx/createinputvcf"
+
+
+    test("human paired end bam - genome.fa") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [id: 'GRCh38'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.vcf[0][1]).name,
+                    process.out.versions).match() }
+            )
+        }
+    }
+
+
+    test("stub") {
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id: 'test'],
+                    [],
+                    []
+                ]
+                input[1] = [
+                    [id: 'test_genome'],
+                    []
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.vcf[0][1]).name,
+                    process.out.versions).match() }
+            )
+        }
+    }
+}

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

@@ -0,0 +1,28 @@
+{
+    "stub": {
+        "content": [
+            "test_variants.vcf.gz",
+            [
+                "versions.yml:md5,6afe5f69d9cb49f74eb1958a8ba2e990"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-10-01T14:20:26.587276"
+    },
+    "human paired end bam - genome.fa": {
+        "content": [
+            "test_variants.vcf.gz",
+            [
+                "versions.yml:md5,6afe5f69d9cb49f74eb1958a8ba2e990"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-10-01T14:10:19.196392"
+    }
+}

modules/nf-core/pypgx/createinputvcf/tests/nextflow.config

@@ -0,0 +1,6 @@
+process {
+        withName: "PYPGX_CREATEINPUTVCF" {
+
+        ext.assembly_version = {"GRCh38"}
+        ext.pgx_genes =  {["GRIK1"]}}
+}

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

@@ -0,0 +1,2 @@
+pypgx/createinputvcf:
+  - "modules/nf-core/pypgx/createinputvcf/**"