include generate_author_sbt in sarscov2_illumina_full wdl workflow

pipes/WDL/workflows/sarscov2_illumina_full.wdl

@@ -33,14 +33,27 @@ workflow sarscov2_illumina_full {
           description: "A post-submission attributes file from NCBI BioSample, which is available at https://submit.ncbi.nlm.nih.gov/subs/ and clicking on 'Download attributes file with BioSample accessions'. The 'sample_name' column must match the external_ids used in sample_rename_map (or internal ids if sample_rename_map is omitted).",
           patterns: ["*.txt", "*.tsv"]
         }
-
+        author_list: {
+          description: "A string containing a space-delimited list with of author surnames separated by first name and (optional) middle initial. Ex. 'Lastname,Firstname, Last-hypenated,First,M., Last,F.'"
+        }
+        author_sbt_defaults_yaml: {
+          description: "A YAML file with default values to use for the submitter, submitter affiliation, and author affiliation. Optionally including authors at the start and end of the author_list. Example: gs://pathogen-public-dbs/other-related/default_sbt_values.yaml",
+          patterns: ["*.yaml","*.yml"]
+        }
+        author_sbt_j2_template: {
+          description: "A jinja2-format template for the sbt file expected by NCBI. Example: gs://pathogen-public-dbs/other-related/author_template.sbt.j2"
+        }
     }
 
     input {
         File          flowcell_tgz
         File          reference_fasta
         String        amplicon_bed_prefix
 
+        String?       author_list # of the form "Lastname,A.B., Lastname,C.,"; optional alternative to names in author_sbt_defaults_yaml
+        File          author_sbt_defaults_yaml # defaults to fill in for author_sbt file (including both author and non-author fields)
+        File          author_sbt_j2_template
+
         Array[File]   biosample_attributes
         String?       instrument_model
         String        sra_title
@@ -325,10 +338,17 @@ workflow sarscov2_illumina_full {
         sequences = submittable_filter.filtered_fasta,
         keep_list = [biosample_to_genbank.sample_ids]
     }
+    call ncbi.generate_author_sbt_file as generate_author_sbt {
+        input:
+            author_list   = author_list,
+            defaults_yaml = author_sbt_defaults_yaml,
+            j2_template   = author_sbt_j2_template
+    }
     call ncbi.package_genbank_ftp_submission {
       input:
         sequences_fasta          = submit_genomes.filtered_fasta,
         source_modifier_table    = biosample_to_genbank.genbank_source_modifier_table,
+        author_template_sbt      = generate_author_sbt.sbt_file,
         structured_comment_table = structured_comments.structured_comment_table,
         submission_name          = flowcell_id,
         submission_uid           = flowcell_id