put rhogs in folder, otherwise sbatch file very big

Author: sinamajidian

FastOMA/batch_roothogs.py

@@ -91,7 +91,7 @@ def folder_1h_rhog(address_rhogs_folder, output_folder_big, output_folder_rest):
 
 def batch_roothogs():
 
-    input_rhog = "./" # rhogs_all
+    input_rhog = "./rhogs_all/" #
     output_folder_big = "./rhogs_big/"
     output_folder_rest = "./rhogs_rest/"
     folder_1h_rhog(input_rhog, output_folder_big, output_folder_rest)

FastOMA/collect_subhogs.py

@@ -6,6 +6,10 @@
 # from . import _config
 from ._config import logger_hog
 
+
+# This code collect subhogs and writes outputs.
+
+
 def collect_subhogs():
 
     logger_hog.info("started collecting pickle files ")
@@ -16,7 +20,7 @@ def collect_subhogs():
     # tr|A0A0N7KCI6|A0A0N7KCI6_ORYSJ
     # for qfo benchamrk, the middle should be wirtten in the file
 
-    pickle_folder = "./" # pickle_rhogs
+    pickle_folder = "./" #pickle_rhogs
     output_xml_name = "./output_hog.orthoxml"
     gene_id_pickle_file = "./gene_id_dic_xml.pickle"
 
@@ -130,7 +134,7 @@ def max_og_tree(tree):
         return og_prot_list
 
     input_orthoxml = output_xml_name # sys.argv[1]  # "out_folder/output_hog_.orthoxml"
-    rhog_all_folder = "./" #sys.argv[2] + "/"  # "out_folder/rhogs_all/"
+    rhog_all_folder = "./rhogs_all/" #sys.argv[2] + "/"  # "out_folder/rhogs_all/"
     fasta_format = "fa"  # of the rhogs_all
 
     output_file_og_tsv = "OrthologousGroups.tsv"

FastOMA_light.nf

@@ -3,7 +3,7 @@ params.input_folder = "./in_folder/"
 params.output_folder = "./out_folder/"
 params.proteome_folder = params.input_folder + "/proteome"
 params.proteomes = params.proteome_folder + "/*"
-params.hogmap_input_folder = params.input_folder + "/hogmap_input_folder"
+params.hogmap_in = params.input_folder + "/hogmap_in"
 
 params.hogmap_folder = params.output_folder + "/hogmap"
 //params.rhogs_folder = params.output_folder + "/rhogs_all"
@@ -39,7 +39,7 @@ process infer_roothogs{   // publishDir  params.rhogs_folder
     path hogmap_folder
     path proteome_folder
   output:
-    path "rhogs_all/*"
+    path "rhogs_all" // path "rhogs_all/*"
     path "gene_id_dic_xml.pickle"
     val true         // nextflow-io.github.io/patterns/state-dependency/
   script:
@@ -52,7 +52,8 @@ process infer_roothogs{   // publishDir  params.rhogs_folder
 process batch_roothogs{ // publishDir params.output_folder
   input:
     val ready_infer_roothogs
-    path rhogs_folder
+    //path rhogs_folder
+    path "rhogs_all"
   output:
     path "rhogs_rest/*", optional: true
     path "rhogs_big/*" , optional: true
@@ -103,7 +104,7 @@ process collect_subhogs{
     val ready_hog_big     // path pickle_rhogs   // this is for depenedcy
     path all_pickles //"*.pickle"  //path "pickle_rhogs"   // this is the folder includes pickles_rhogs
     path "gene_id_dic_xml.pickle"
-    path rhogs_folder
+    path "rhogs_all"
   output:
     path "output_hog.orthoxml"
     path "OrthologousGroupsFasta"
@@ -123,21 +124,20 @@ workflow {
 //    rhogs_folder = Channel.fromPath(params.rhogs_folder)
 
     genetrees_folder = Channel.fromPath(params.genetrees_folder)
-    hogmap_input_folder = Channel.fromPath(params.hogmap_input_folder)
+    hogmap_in = Channel.fromPath(params.hogmap_in)
 
 //    pickles_rhogs_folder =  Channel.fromPath(params.pickles_rhogs_folder)
     omamerdb = Channel.fromPath(params.input_folder+"/omamerdb.h5")     // proteomes.view{"prot ${it}"}
     proteomes_omamerdb = proteomes.combine(omamerdb)
-    proteomes_omamerdb_inputhog = proteomes_omamerdb.combine(hogmap_input_folder) // proteomes_omamerdb_inputhog.view{" rhogsbig ${it}"}
+    proteomes_omamerdb_inputhog = proteomes_omamerdb.combine(hogmap_in) // proteomes_omamerdb_inputhog.view{" rhogsbig ${it}"}
     (hogmap, ready_omamer_run)= omamer_run(proteomes_omamerdb_inputhog)
     ready_omamer_run_c = ready_omamer_run.collect()
 
-    (rhogs, gene_id_dic_xml, ready_infer_roothogs) = infer_roothogs(ready_omamer_run_c, hogmap_folder, proteome_folder)
+    (rhogs_folder, gene_id_dic_xml, ready_infer_roothogs) = infer_roothogs(ready_omamer_run_c, hogmap_folder, proteome_folder)
+    // rhogs_folder and "rhogs_all" are the same
     ready_infer_roothogs_c = ready_infer_roothogs.collect()
 
-    // old :  (rhogs_rest_list, rhogs_big_list, ready_batch_roothogs) = batch_roothogs(ready_infer_roothogs_c, rhogs_folder)
-
-    (rhogs_rest_list, rhogs_big_list, ready_batch_roothogs) = batch_roothogs(ready_infer_roothogs_c, rhogs)
+    (rhogs_rest_list, rhogs_big_list, ready_batch_roothogs) = batch_roothogs(ready_infer_roothogs_c, rhogs_folder)
     ready_batch_roothogs_c = ready_batch_roothogs.collect()
 
     species_tree = Channel.fromPath(params.species_tree)
@@ -152,7 +152,7 @@ workflow {
     (pickle_rest_rhog,  msas_out_rest, genetrees_out_test, ready_hog_rest) = hog_rest(rhogsrest_tree_ready)
     all_pickles = pickle_big_rhog.mix(pickle_rest_rhog).collect() // all_pickles.view() //     pickle_rhogs_folder = Channel.fromPath(params.output_folder+"/pickle_rhogs")
 
-    (orthoxml_file, OrthologousGroupsFasta, OrthologousGroups_tsv, rootHOGs_tsv)  = collect_subhogs(ready_hog_rest.collect(), ready_hog_big.collect(), all_pickles, gene_id_dic_xml, rhogs)  // pickles_rhogs_folder
+    (orthoxml_file, OrthologousGroupsFasta, OrthologousGroups_tsv, rootHOGs_tsv)  = collect_subhogs(ready_hog_rest.collect(), ready_hog_big.collect(), all_pickles, gene_id_dic_xml, rhogs_folder)  // pickles_rhogs_folder
     orthoxml_file.view{" output orthoxml file ${it}"}
 
 }