Add snpclustering subworkflow

subworkflows/nf-core/snpclustering/main.nf

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+#!/usr/bin/env nextflow
+nextflow.enable.dsl = 2
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT NF-CORE MODULES
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { BCFTOOLS_FILTER       } from '../../../modules/nf-core/bcftools/filter/main'
+include { PLINK2_INDEP_PAIRWISE } from '../../../modules/nf-core/plink2/indeppairwise/main'
+include { PLINK2_RECODE_VCF     } from '../../../modules/nf-core/plink2/recodevcf/main'
+include { FLASHPCA2             } from '../../../modules/nf-core/flashpca2/main'
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    SUBWORKFLOW
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+workflow SNPCLUSTERING {
+    take:
+    meta
+    vcf
+    vcf_index
+    maf
+    missing
+
+    main:
+    versions = Channel.empty()
+
+    BCFTOOLS_FILTER ( vcf.join(vcf_index), maf, missing )
+    versions = versions.mix(BCFTOOLS_FILTER.out.versions.first())
+
+    PLINK2_INDEP_PAIRWISE ( BCFTOOLS_FILTER.out.vcf )
+    versions = versions.mix(PLINK2_INDEP_PAIRWISE.out.versions.first())
+
+    PLINK2_RECODE_VCF ( PLINK2_INDEP_PAIRWISE.out.pgen )
+    versions = versions.mix(PLINK2_RECODE_VCF.out.versions.first())
+
+    FLASHPCA2 ( PLINK2_RECODE_VCF.out.vcf )
+    versions = versions.mix(FLASHPCA2.out.versions.first())
+
+    // TODO: qui aggiungeremo KMeans/DBSCAN/plot quando creeremo i moduli local
+
+    emit:
+    cluster_labels = Channel.empty()   // placeholder
+    metrics        = Channel.empty()   // placeholder
+    plots          = Channel.empty()
+    versions       = versions
+}

subworkflows/nf-core/snpclustering/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/nf-core/meta-schema.json
+
+name: "snpclustering"
+description: "End-to-end unsupervised clustering of genomic samples starting from multi-sample VCF files. Performs variant filtering (MAF + missingness), optional LD pruning, PCA (FlashPCA2 or IncrementalPCA), KMeans/DBSCAN clustering and internal validation."
+keywords:
+  - genomics
+  - clustering
+  - unsupervised clustering
+  - VCF
+  - nf-core
+authors:
+  - "Donald Baku (@dbaku42)"
+components:
+  - bcftools/filter
+  - plink2/indep/pairwise
+  - plink2/recode/vcf
+  - plink2/indeppairwise
+  - plink2/recodevcf
+  - flashpca2
+input:
+  - meta:
+      type: map
+      description: "Groovy Map containing sample metadata"
+  - vcf:
+      type: file
+      description: "Multi-sample VCF file (bgzipped and indexed)"
+      pattern: "*.{vcf,vcf.gz}"
+  - vcf_index:
+      type: file
+      description: "Index of the VCF file (.tbi or .csi)"
+      pattern: "*.{tbi,csi}"
+  - maf:
+      type: float
+      description: "Minimum minor allele frequency threshold"
+      default: 0.01
+  - missing:
+      type: float
+      description: "Maximum missingness threshold"
+      default: 0.10
+output:
+  - meta:
+      type: map
+      description: "Groovy Map containing sample metadata"
+  - cluster_labels:
+      type: file
+      description: "CSV file with per-sample cluster assignments"
+      pattern: "cluster_labels.csv"
+  - metrics:
+      type: file
+      description: "Table with all cluster quality metrics"
+      pattern: "*_metrics.tsv"
+  - plots:
+      type: file
+      description: "Directory containing publication-ready plots"
+      pattern: "plots/"
+  - versions:
+      type: file
+      description: "File containing versions of all tools used"
+      pattern: "versions.yml"

subworkflows/nf-core/snpclustering/tests/main.nf.test

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+nextflow_workflow {
+
+    name "Test Workflow SNPCLUSTERING"
+    script "../main.nf"
+    workflow "SNPCLUSTERING"
+    config "./nextflow.config"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/snpclustering"
+    tag "bcftools/filter"
+    tag "plink2/indeppairwise"
+    tag "plink2/recodevcf"
+    tag "flashpca2"
+
+    test("vcf.gz input") {
+
+        when {
+            workflow {
+                """
+                input[0] = [ id:'test' ]
+                input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.vcf.gz', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                input[3] = 0.01
+                input[4] = 0.10
+                """
+            }
+        }
+
+        then {
+            assert workflow.success
+        }
+    }
+}

subworkflows/nf-core/snpclustering/tests/tags.yml

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+subworkflows/snpclustering:
+  - subworkflows/nf-core/snpclustering/**