include entire isolate name in genbank metadata

theiagen · Apr 1, 2021 · 9aec072 · 9aec072
1 parent 61c5f60
commit 9aec072
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/tasks/task_pe_pub_repo_submission.wdl b/tasks/task_pe_pub_repo_submission.wdl
@@ -146,7 +146,7 @@ task genbank {
 
     echo Sequence_ID,Country,Host,Isolate,Collection Date, BioProject Accession > ~{submission_id}.genbankMeta.csv
 
-    echo "\"~{submission_id}\",\"~{iso_country}\",\"~{iso_host}\",\"${isolate}\",\"~{collection_date}\",\"~{BioProject}\"" >> ~{submission_id}.genbankMeta.csv
+    echo "\"~{submission_id}\",\"~{iso_country}\",\"~{iso_host}\",\"~{submission_id}\",\"~{collection_date}\",\"~{BioProject}\"" >> ~{submission_id}.genbankMeta.csv
 
   >>>
 

diff --git a/tasks/task_se_pub_repo_submission.wdl b/tasks/task_se_pub_repo_submission.wdl
@@ -146,7 +146,7 @@ task genbank {
 
     echo Sequence_ID,Country,Host,Isolate,Collection Date, BioProject Accession > ~{submission_id}.genbankMeta.csv
 
-    echo "\"~{submission_id}\",\"~{iso_country}\",\"~{iso_host}\",\"${isolate}\",\"~{collection_date}\",\"~{BioProject}\"" >> ~{submission_id}.genbankMeta.csv
+    echo "\"~{submission_id}\",\"~{iso_country}\",\"~{iso_host}\",\"~{submission_id}\",\"~{collection_date}\",\"~{BioProject}\"" >> ~{submission_id}.genbankMeta.csv
 
   >>>
-Original file line number
+Diff line change
@@ Expand Up / @@ -146,7 +146,7 @@ task genbank { @@
         echo Sequence_ID,Country,Host,Isolate,Collection Date, BioProject Accession > ~{submission_id}.genbankMeta.csv
-        echo "\"~{submission_id}\",\"~{iso_country}\",\"~{iso_host}\",\"${isolate}\",\"~{collection_date}\",\"~{BioProject}\"" >> ~{submission_id}.genbankMeta.csv
+        echo "\"~{submission_id}\",\"~{iso_country}\",\"~{iso_host}\",\"~{submission_id}\",\"~{collection_date}\",\"~{BioProject}\"" >> ~{submission_id}.genbankMeta.csv
       >>>
@@ Expand Down @@