Feature/prs modules

.nf-core.yml

@@ -1,4 +1,10 @@
 org_path: UMCUGenetics
 repository_type: modules
 lint:
-  environment_yml
+  main_nf:
+    - when_exist
+    - test_main_tags
+    - container_links
+  module_tests:
+    - test_main_tags
+  meta_yml: false

modules/UMCUGenetics/knn/calc/main.nf

@@ -0,0 +1,33 @@
+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
+
+    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
+    """
+}