fix naming scheme

Author: luisas

subworkflows/local/align.nf

@@ -382,7 +382,7 @@ workflow ALIGN {
         ch_msa.map{ meta, msa -> [ meta["id"], msa]}
             .groupTuple()
             .filter{ it[1].size() > 1 }
-            .map{ id_meta, msas -> [ ["id": id_meta, "tree":"", "args_tree":"", "args_tree_clean":null, "aligner":"CONSENSUS", "args_aligner":"", "args_aligner_clean":null ], msas ]}
+            .map{ id_meta, msas -> [ ["id": id_meta, "tree":"DEFAULT", "args_tree":"", "args_tree_clean":"default", "aligner":"CONSENSUS", "args_aligner":"", "args_aligner_clean":"default" ], msas ]}
             .set{ ch_msa_consensus }
 
         CONSENSUS(ch_msa_consensus, [[:],[]], compress)

subworkflows/local/utils_nfcore_multiplesequencealign_pipeline/main.nf

@@ -75,7 +75,7 @@ workflow PIPELINE_INITIALISATION {
                         def tree_map = [:]
                         def align_map = [:]
 
-                        tree_map["tree"] = meta_clone["tree"]
+                        tree_map["tree"] = Utils.clean_tree(meta_clone["tree"])
                         tree_map["args_tree"] = meta_clone["args_tree"]
                         tree_map["args_tree_clean"] = Utils.cleanArgs(meta_clone.args_tree)