File_formats: removed redundant nw

lib/detection_pipeline.ml

@@ -19,7 +19,7 @@ module type S = sig
 
   val amino_acid_alignment : query -> aminoacid_fasta file
 
-  val gene_tree : query -> nw file
+  val gene_tree : query -> newick file
 
   val dn_tree : query -> text file
 

lib/detection_pipeline.mli

@@ -19,7 +19,7 @@ module type S = sig
 
   val amino_acid_alignment : query -> aminoacid_fasta file
 
-  val gene_tree : query -> nw file
+  val gene_tree : query -> newick file
 
   val dn_tree : query -> text file
 

lib/file_formats.ml

@@ -20,11 +20,6 @@ class type phylip = object
   method format : [`phylip]
 end
 
-class type nw = object
-  inherit text
-  method format : [`nw]
-end
-
 class type diffsel_tree = object
   inherit text
   method format : [`diffsel_tree]

lib/phyml.ml

@@ -36,5 +36,5 @@ let phyml ~model ~tree phy : [`phyml] directory =
     ]
   ]
 
-let phyml_tree ~model ~tree phy : nw file =
+let phyml_tree ~model ~tree phy : newick file =
   Workflow.select (phyml ~model ~tree phy) ["tree.phy_phyml_tree.txt"]

lib/post_analyses.ml

@@ -43,8 +43,8 @@ type dn_ds_tsv = {
 }
 
 type reinfered_trees = {
-  reinfered_tree_nt : nw file ;
-  reinfered_tree_aa : nw file ;
+  reinfered_tree_nt : newick file ;
+  reinfered_tree_aa : newick file ;
   input_tree : nhx file ;
   tree_prefix : string ;
   model_prefix : string ;

lib/tree_dataset.mli

@@ -32,5 +32,5 @@ val raxmlng_fna :
   ?model : string ->
   fna: nucleotide_fasta file ->
   unit ->
-  nw file
+  newick file