Add ancestry information to pgs report

Author: lukfor

modules/local/pgs_calculation/create_html_report.nf

@@ -1,32 +1,34 @@
 process CREATE_HTML_REPORT {
 
-  publishDir params.output, mode: 'copy'
+    publishDir params.output, mode: 'copy'
 
-  input:
+    input:
     path(merged_score)
     path(merged_info)
     path(scores_meta)
+    path(estimated_ancestry)
 
-
-  output:
+    output:
     path "*.html", emit: html_report
     path "*.coverage.txt", emit: coverage_report
 
-  """
-
-  pgs-calc report \
-    --data ${merged_score} \
-    --info ${merged_info} \
-    --meta ${scores_meta} \
-    --out scores.html
-
-  pgs-calc report \
-    --data ${merged_score} \
-    --info ${merged_info} \
-    --meta ${scores_meta} \
-    --template txt \
-    --out scores.coverage.txt
-
-  """
+    script:
+    samples = params.ancestry.enabled ? "--samples ${estimated_ancestry}" : ""
+
+    """
+    pgs-calc report \
+        --data ${merged_score} \
+        --info ${merged_info} \
+        --meta ${scores_meta} \
+        $samples \
+        --out scores.html
+
+    pgs-calc report \
+        --data ${merged_score} \
+        --info ${merged_info} \
+        --meta ${scores_meta} \
+        --template txt \
+        --out scores.coverage.txt
+    """
 
 }

workflows/pgs_calculation.nf

@@ -29,7 +29,8 @@ workflow PGS_CALCULATION {
     CREATE_HTML_REPORT(
         MERGE_CHUNKS_SCORES.out.collect(),
         MERGE_CHUNKS_INFOS.out.collect(),
-        file(params.pgscatalog.meta, checkIfExists:true)
+        file(params.pgscatalog.meta, checkIfExists:true),
+        estimated_ancestry.collect().ifEmpty([])
     )
 
 }