From a8a6d8b5f8f40d8f1dff111ada2987f1917af9c0 Mon Sep 17 00:00:00 2001
From: Daniel Park <dpark@broadinstitute.org>
Date: Fri, 25 Aug 2023 12:59:07 +0200
Subject: [PATCH] more tolerant if no isolate name defined

---
 pipes/WDL/tasks/tasks_ncbi_tools.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pipes/WDL/tasks/tasks_ncbi_tools.wdl b/pipes/WDL/tasks/tasks_ncbi_tools.wdl
index 64d0328db..8d0cd42ca 100644
--- a/pipes/WDL/tasks/tasks_ncbi_tools.wdl
+++ b/pipes/WDL/tasks/tasks_ncbi_tools.wdl
@@ -92,7 +92,7 @@ task Fetch_SRA_to_BAM {
         biosample['accession'] = meta['EXPERIMENT_PACKAGE_SET']['EXPERIMENT_PACKAGE']['SAMPLE']['IDENTIFIERS']['EXTERNAL_ID']['content']
         biosample['message'] = 'Successfully loaded'
         biosample['bioproject_accession'] = meta['EXPERIMENT_PACKAGE_SET']['EXPERIMENT_PACKAGE']['STUDY']['IDENTIFIERS']['EXTERNAL_ID']['content']
-        biosample['sample_name'] = biosample['isolate']
+        biosample['sample_name'] = biosample.get('isolate', biosample.get('Sample Name', biosample.get('strain', '')))
         for k,v in biosample.items():
             if v == 'not provided':
                 biosample[k] = ''