genbank src updates

broadinstitute · Jan 14, 2025 · 81c1aa7 · 81c1aa7
1 parent c45ba1c
commit 81c1aa7
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Showing 2 changed files with 21 additions and 3 deletions.
diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl
@@ -764,6 +764,7 @@ task biosample_to_genbank {
     File?   filter_to_ids
     String? filter_to_accession
     Map[String,String] src_to_attr_map = {}
+    String?  organism_name_override
 
     Boolean sanitize_seq_ids = true
 
@@ -811,10 +812,24 @@ task biosample_to_genbank {
         and (not samples_to_filter_to or row[header_key_map['Sequence_ID']] in samples_to_filter_to))
       print("filtered to {} samples".format(len(biosample_attributes)))
 
+    # override organism_name if provided (this allows us to submit Genbank assemblies for
+    # specific species even though the metagenomic BioSample may have been registered with a different
+    # species or none at all)
+    if "~{default='' organism_name_override}":
+        for row in biosample_attributes:
+            row['organism'] = "~{default='' organism_name_override}"
+
     # handle special submission types: flu, sc2, noro, dengue
-    for special in ('Influenza A virus', 'Influenza B virus', 'Influenza C virus',
+    special_bugs = ('Influenza A virus', 'Influenza B virus', 'Influenza C virus',
                     'Severe acute respiratory syndrome coronavirus 2',
-                    'Norovirus', 'Dengue virus'):
+                    'Norovirus', 'Dengue virus')
+    for special in special_bugs:
+        # sanitize organism name if it's a special one
+        for row in biosample_attributes:
+          if row['organism'].startswith(special):
+              row['organism'] = special
+
+        # enforce that special submissions are all the same special thing
         if any(row['organism'] == special for row in biosample_attributes):
           print("special organism found " + special)
           assert all(row['organism'] == special for row in biosample_attributes), "if any samples are {}, all samples must be {}".format(special, special)

diff --git a/pipes/WDL/workflows/genbank_single.wdl b/pipes/WDL/workflows/genbank_single.wdl
@@ -23,7 +23,10 @@ workflow genbank_single {
         Int           tax_id
 
         String        email_address # required for fetching data from NCBI APIs
-        File?         biosample_attributes_tsv # if empty, we will fetch from NCBI via accession
+
+        #String?       biosample_attributes_json # if this is used, we will use this first
+        File?         biosample_attributes_tsv # if no json, we will read this tsv
+        # if both are unspecified, we will fetch from NCBI via biosample_accession
     }
 
     parameter_meta {