Plinkpca

modules/nf-core/plink2/pca/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::plink2=2.00a5.10"

modules/nf-core/plink2/pca/main.nf

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+process PLINK2_PCA {
+    tag "$meta.id"
+    label 'process_single'
+    conda "${moduleDir}/environment.yml"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/plink2:2.00a5.10--h4ac6f70_0'
+        : 'biocontainers/plink2:2.00a5.10--h4ac6f70_0'}"
+
+    input:
+    tuple val(meta), val(npcs), val(use_approx), path(pgen), path(psam), path(pvar)
+
+    output:
+    tuple val(meta), path("*.eigenvec"), emit: evecfile
+    tuple val(meta), path("*.eigenval"), emit: evfile
+    tuple val(meta), path("*.log"), emit: logfile
+    path "versions.yml", emit: versions
+
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def approx_option = use_approx ? "approx" : ""
+    def n_pcs = npcs ? npcs : 10
+    """
+    plink2 \\
+        --pca ${n_pcs} ${approx_option} \\
+        --memory ${task.memory.toMega()} \\
+        $args \\
+        --threads $task.cpus \\
+        --pfile ${pgen.baseName} \\
+        --out ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        plinkpca: \$(plink2 --version |& sed '1!d ; s/plink2 //')
+    END_VERSIONS
+    """
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.eigenvec ${prefix}.eigenval
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        plink2: \$(plink2 --version 2>&1 | sed 's/^PLINK v//; s/ 64.*\$//' )
+    END_VERSIONS
+    """
+}

modules/nf-core/plink2/pca/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "plink2_pca"
+description: Perform PCA analysis using PLINK
+keywords:
+  - plink2
+  - pca
+  - plink2_pca
+
+tools:
+  - plink2:
+      description: |
+        Whole genome association analysis toolset, designed to perform a range
+        of basic, large-scale analyses in a computationally efficient manner
+      homepage: http://www.cog-genomics.org/plink/2.0/
+      documentation: http://www.cog-genomics.org/plink/2.0/general_usage
+      doi: "10.1186/s13742-015-0047-8"
+      licence: ["GPL v3"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - npcs:
+        type: integer
+        description: Number of PCs to compute
+    - use_approx:
+        type: boolean
+        description: If true, use the approximate method
+    - pgen:
+        type: file
+        description: PLINK 2 binary genotype table
+        pattern: "*.{pgen}"
+    - psam:
+        type: file
+        description: PLINK 2 sample information file
+        pattern: "*.{psam}"
+    - pvar:
+        type: file
+        description: PLINK 2 variant information file
+        pattern: "*.{pvar}"
+
+output:
+  - evecfile:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+          pattern: "*.eigenvec"
+      - "*.eigenvec":
+          type: map
+          description: |
+            Groovy Map containing sample information
+          pattern: "*.eigenvec"
+  - evfile:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+          pattern: "*.eigenval"
+      - "*.eigenval":
+          type: map
+          description: |
+            Groovy Map containing sample information
+          pattern: "*.eigenval"
+  - logfile:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+          pattern: "*.log"
+      - "*.log":
+          type: map
+          description: |
+            Groovy Map containing sample information
+          pattern: "*.log"
+  - versions:
+      - versions.yml:
+          type: file
+          description: |
+            File containing the version of the program
+          pattern: "versions.yml"
+authors:
+  - "@bruno-ariano"
+maintainers:
+  - "@bruno-ariano"

modules/nf-core/plink2/pca/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process PLINK2_PCA"
+    script "../main.nf"
+    process "PLINK2_PCA"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "plink2"
+    tag "plink2/pca"
+
+    test("plink2_pca") {
+        config "./nextflow.config"
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id: 'pca' ], // meta map!
+                    10,
+                    true,
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.pgen', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.pvar', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/popgen/plink_simulated.psam', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert process.out.evecfile.get(0).get(1) ==~ ".*.eigenvec" },
+                { assert process.out.evfile.get(0).get(1) ==~ ".*.eigenval" },
+                { assert process.out.logfile.get(0).get(1) ==~ ".*.log" },
+                { assert snapshot(process.out.versions).match("versions") }
+
+            )
+        }
+    }
+}

modules/nf-core/plink2/pca/tests/main.nf.test.snap

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+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,6aad532ec6f7666e23d269c394e1d796"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-26T14:48:24.762736992"
+    }
+}

modules/nf-core/plink2/pca/tests/nextflow.config

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+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/
+process {
+    withName: PLINK2_PCA {
+        ext.prefix = { "${meta.id}.pca" }
+    }
+}

modules/nf-core/plink2/pca/tests/tags.yml

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+plink2/pca:
+  - modules/nf-core/plink2/pca/**