From f62f8bb1e1c45dad993d2dd36f75b1bf04fd2477 Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Tue, 6 Sep 2022 14:14:28 +0200
Subject: [PATCH] Fix vcf files in helix export file.

---
 clarity_epp/export/workflow.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/clarity_epp/export/workflow.py b/clarity_epp/export/workflow.py
index 66c99e2..a399c4d 100644
--- a/clarity_epp/export/workflow.py
+++ b/clarity_epp/export/workflow.py
@@ -79,8 +79,13 @@ def helix_magnis(lims, process_id, output_file):
                 exomedepth_vcf = ''
                 if 'Dx GATK vcf' in artifact.udf:
                     gatk_vcf = artifact.udf['Dx GATK vcf']
+                elif 'Dx GATK vcf' in artifact.input_artifact_list()[0].udf:  # Look one more step back.
+                    gatk_vcf = artifact.input_artifact_list()[0].udf['Dx GATK vcf']
+
                 if 'Dx ExomeDepth vcf' in artifact.udf:
                     exomedepth_vcf = artifact.udf['Dx ExomeDepth vcf']
+                elif 'Dx ExomeDepth vcf' in artifact.input_artifact_list()[0].udf:  # Look one more step back.
+                    exomedepth_vcf = artifact.input_artifact_list()[0].udf['Dx ExomeDepth vcf']
 
                 output_file.write((
                     "{meet_id}\t{werklijst}\t{onderzoeksnummer}\t{monsternummer}\t{meetw_zui}\t{meetw_zui_herh}\t"