Feature/variant calling prs

.gitignore

@@ -1,24 +1,17 @@
-# Compiled class file
-*.class
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc
+null/
+\#*
 
-# Log file
-*.log
+# NF-test
+.nf-test/
+.nf-test/*
+.nf-test*
 
-# BlueJ files
-*.ctxt
-
-# Mobile Tools for Java (J2ME)
-.mtj.tmp/
-
-# Package Files #
-*.jar
-*.war
-*.nar
-*.ear
-*.zip
-*.tar.gz
-*.rar
-
-# virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
-hs_err_pid*
-replay_pid*
+modules/nf-core

modules/UMCUGenetics/ancestry_knn/calc/main.nf

@@ -0,0 +1,34 @@
+process ANCESTRY_KNN {
+    tag "${meta.id}"
+    label "process_medium"
+
+    container "ghcr.io/astral-sh/uv:python3.13-bookworm"
+
+    input:
+    tuple val(meta), path(eigenvec)
+    tuple val(meta2), path(ref_metadata)
+
+    output:
+    tuple val(meta), path("*_knn.tsv"), emit: knn_tsv
+    tuple val(meta), path("*_knn_pca.png"), emit: knn_pca_plot, optional: true
+    tuple val("${task.process}"), val('ancestry_knn'), eval('echo 1.0.0'), emit: versions_ancestry_knn, topic: versions
+
+    script:
+    def prefix = task.ext.prefix ?: meta.id
+    def args = task.ext.args ?: ""
+    """
+    knn.py \
+        --eig ${eigenvec} \\
+        --labels ${ref_metadata} \\
+        ${args} \\
+        --plot-output ${prefix}_knn_pca.png \\
+        --output ${prefix}_knn.tsv
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: meta.id
+    """
+    touch ${prefix}_knn.tsv
+    touch ${prefix}_knn_pca.png
+    """
+}