Merge pull request #99 from eastgenomics/DI-141_gather_sentieonVCF

Update logic for finding sentieon VCFs (#99)
eastgenomics · May 11, 2023 · 19deb23 · 19deb23
2 parents 04dca92 + 2f760a8
commit 19deb23
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/reports.py b/reports.py
@@ -75,7 +75,7 @@ def run_reports(
     ### Identify samples to run reports workflow for
     # Gather sample names that have a Sentieon VCF generated
     ## current pattern picks up both "normal" and "genomic" VCFs
-    sentieon_folder_path = find_app_dir(ss_workflow_out_dir, assay_config.cnvcalling_input_dict["app"])
+    sentieon_folder_path = find_app_dir(ss_workflow_out_dir, "sentieon")
     single_sample_vcfs = find_files(
         project_name, sentieon_folder_path, pattern="(.*).vcf.gz$"
     )