Added ref_name as a sawfish_call input to parse filenames.

wdl-ci.config.json

@@ -2396,6 +2396,7 @@
                 ],
                 "ref_fasta": "${ref_fasta}",
                 "ref_index": "${ref_index}",
+                "ref_name": "${ref_name}",
                 "out_prefix": "HG002.GRCh38.structural_variants",
                 "runtime_attributes": "${default_runtime_attributes}"
               },
@@ -2436,6 +2437,7 @@
                 ],
                 "ref_fasta": "${ref_fasta}",
                 "ref_index": "${ref_index}",
+                "ref_name": "${ref_name}",
                 "out_prefix": "HG002-trio.joint.GRCh38.structural_variants",
                 "runtime_attributes": "${default_runtime_attributes}"
               },

workflows/joint/joint.wdl

@@ -82,6 +82,7 @@ workflow joint {
       aligned_bam_indices = aligned_bam_indices,
       ref_fasta           = ref_map["fasta"],                                      # !FileCoercion
       ref_index           = ref_map["fasta_index"],                                # !FileCoercion
+      ref_name            = ref_map["name"],
       out_prefix          = "~{family_id}.joint.~{ref_map['name']}.structural_variants",
       runtime_attributes  = default_runtime_attributes
   }

workflows/upstream/upstream.wdl

@@ -194,6 +194,7 @@ workflow upstream {
         aligned_bam_indices = [aligned_bam_index],
         ref_fasta           = ref_map["fasta"],                                      # !FileCoercion
         ref_index           = ref_map["fasta_index"],                                # !FileCoercion
+        ref_name            = ref_map["name"],
         out_prefix          = "~{sample_id}.~{ref_map['name']}.structural_variants",
         runtime_attributes  = default_runtime_attributes
     }