further refactoring bppseqgen

lib/bppsuite.ml

@@ -130,13 +130,14 @@ rate_distribution=Constant()
 
 |}
 
-  let multi_profiles ?(descr="") ~profile_f ~profile_c ~tree ~tree_dataset ~hypothesis ~ne_c ~ne_a ~seed =
+  let multi_profiles ?(descr="") ~profile_f ~profile_c ~tree_dataset ~hypothesis ~ne_c ~ne_a ~seed =
     let nb_sites_per_profile = 1 in
     (* let nb_combis = Pervasives.(nb_sites / nb_sites_per_profile) in *)
     let config_f = dest // "config.bpp" in
     (* let profile_c_ok = tmp // "profiles_c.tsv" in *)
     let profile_c_ok = dep profile_c in
     let out = dest // "seq.fa" in
+    let tree = Tree_dataset.tree tree_dataset `Simulation in
     let nodes = Tree_dataset.nodes tree_dataset hypothesis in
     workflow ~descr:("bppsuite.bppseqgen" ^ descr) [
       docker env (

lib/bppsuite.mli

@@ -7,7 +7,6 @@ module Bppseqgen : sig
     ?descr : string ->
     profile_f: text_file workflow ->
     profile_c: text_file workflow ->
-    tree:nhx workflow ->
     tree_dataset:[`tree_dataset] directory workflow ->
     hypothesis:Convergence_hypothesis.t ->
     ne_c: float ->

lib/pipeline.ml

@@ -53,7 +53,6 @@ let calc_fixed_seed ~(str:string) (seed:int) : int =
 
 let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~preview ~ns ~seed =
   let model_prefix = Convergence_hypothesis.string_of_model model in
-  let tree = Tree_dataset.tree tree_dataset `Simulation in
   let descr = "."^model_prefix^"."^tree_prefix in
   (* only 1 profile or 1 couple of profiles*)
   (*let config = Convergence_hypothesis.bpp_config nodes model in
@@ -67,7 +66,7 @@ let derive_from_model ~model ~input_tree ~tree_dataset ~tree_prefix ~profile ~pr
   let profile_c = profile.profile_c in
   (*let seed = Random.int Int.max_value in*)
   let seed = calc_fixed_seed ~str:descr seed in
-  let run_fna = Bppsuite.Bppseqgen.multi_profiles ~descr ~tree ~tree_dataset ~hypothesis:model ~profile_f ~profile_c ~ne_c ~ne_a ~seed in
+  let run_fna = Bppsuite.Bppseqgen.multi_profiles ~descr ~tree_dataset ~hypothesis:model ~profile_f ~profile_c ~ne_c ~ne_a ~seed in
   let fna = Bppsuite.Bppseqgen.alignment run_fna in
   let fna_infos = Some (Bppsuite.Bppseqgen.info run_fna) in