start work on new workflow not done yet

Author: dpark01

pipes/WDL/workflows/submit_genbank.wdl

@@ -0,0 +1,41 @@
+version 1.0
+
+import "../tasks/tasks_ncbi_tools.wdl" as ncbi_tools
+import "../tasks/tasks_terra.wdl" as terra
+
+workflow submit_sra {
+    meta {
+        description: "Submit FTP-eligible genomes to NCBI Genbank (currently only flu A/B/C and SARS-CoV-2)"
+        author: "Broad Viral Genomics"
+        email:  "viral-ngs@broadinstitute.org"
+        allowNestedInputs: true
+    }
+
+    input {
+        #Array[File]  submission_files
+        String       batch_id
+
+        File         genbank_xml
+        File         genbank_zip
+
+        File         ncbi_ftp_config_js
+        String       prod_test = "Production" # Production or Test
+    }
+
+    String prefix = "/~{prod_test}/~{batch_id}"
+
+    # TO DO: work in progress, not ready yet
+
+    call ncbi_tools.ncbi_sftp_upload as genbank_upload {
+        input:
+            config_js        = ncbi_ftp_config_js,
+            submission_xml   = genbank_xml,
+            additional_files = [genbank_zip],
+            target_path      = "~{prefix}/genbank",
+            wait_for         = "1"
+    }
+
+    output {
+        Array[File]    genbank_response   = genbank_upload.reports_xmls
+    }
+}

pipes/WDL/workflows/submit_sra.wdl

@@ -25,7 +25,6 @@ workflow submit_sra {
 
     String prefix = "/~{prod_test}/~{flowcell_id}"
 
-
     call terra.gcs_copy as gcs_sra_dump_reads {
         input:
             infiles        = reads_bams,