expose assembly_method and assembly_method_version

broadinstitute · May 18, 2020 · 0914c83 · 0914c83
1 parent e8e796b
commit 0914c83
Showing 1 changed file with 14 additions and 0 deletions.
diff --git a/pipes/WDL/tasks/tasks_ncbi.wdl b/pipes/WDL/tasks/tasks_ncbi.wdl
@@ -159,6 +159,8 @@ task prepare_genbank {
     String?      comment
     String?      organism
     String?      molType
+    String?      assembly_method
+    String?      assembly_method_version
 
     Int?         machine_mem_gb
     String       docker="quay.io/broadinstitute/viral-phylo"
@@ -198,6 +200,12 @@ task prepare_genbank {
     molType: {
       description: "The type of molecule being described. Any value allowed by the INSDC controlled vocabulary may be used here. Valid values are described at http://www.insdc.org/controlled-vocabulary-moltype-qualifier"
     }
+    assembly_method: {
+      description: "Very short description of the software approach used to assemble the genome. We typically provide a github link here. If this is specified, assembly_method_version should also be specified."
+    }
+    assembly_method_version: {
+      description: "The version of the software used. If this is specified, assembly_method should also be specified."
+    }
     comment: {
       description: "Optional comments that can be displayed in the COMMENT section of the Genbank record. This may include any disclaimers about assembly quality or notes about pre-publication availability or requests to discuss pre-publication use with authors."
     }
@@ -226,6 +234,12 @@ task prepare_genbank {
       echo "--mol_type" >> special_args
       echo "${molType}" >> special_args
     fi
+    if [ -n "${assembly_method}" -a -n "${assembly_method_version}" ]; then
+      echo "--assembly_method" >> special_args
+      echo "${assembly_method}" >> special_args
+      echo "--assembly_method_version" >> special_args
+      echo "${assembly_method_version}" >> special_args
+    fi
     if [ -n "${coverage_table}" ]; then
       echo -e "sample\taln2self_cov_median" > coverage_table.txt
       cat ${coverage_table} >> coverage_table.txt