diff --git a/FastOMA.nf b/FastOMA.nf
index e77fe65..a7401c4 100644
--- a/FastOMA.nf
+++ b/FastOMA.nf
@@ -1,229 +1,165 @@
 
-
+// NXF_WRAPPER_STAGE_FILE_THRESHOLD='50000'
 
 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"
+//params.rhogs_folder = params.output_folder + "/rhogs_all"
 params.species_tree = params.input_folder + "/species_tree.nwk"
-params.pickles_rhogs_folder = params.output_folder + "/pickle_rhogs"
+//params.pickles_rhogs_folder = params.output_folder + "/pickle_rhogs"
 params.genetrees_folder = params.output_folder + "/genetrees"
 
 
-// https://github.com/nextflow-io/nextflow/issues/1629
-// https://www.nextflow.io/docs/latest/process.html?highlight=cache#cache
-
-// todo clean up this file
-
 process omamer_run{
   time {4.h}
-  memory {50.GB}
-  cpus  10
+  memory {16.GB}
   publishDir params.hogmap_folder
   input:
-  path proteomes_omamerdb_inputhog
+    path proteomes_omamerdb_inputhog
   output:
-  path "*.hogmap"
-  val true      // ready_omamer_run
+    path "*.hogmap"
+    val true
   script:
-  //   omamer search --db ${proteomes_omamerdb[1]} --query ${proteomes_omamerdb[0]} --nthreads 1  --out ${proteomes_omamerdb[0]}.hogmap
-  // cp /work/FAC/FBM/DBC/cdessim2/default/smajidi1/qfo_hogmap/${proteomes_omamerdb[0]}.hogmap .
   """
     if [ -f ${proteomes_omamerdb_inputhog[2]}/${proteomes_omamerdb_inputhog[0]}.hogmap ]
     then
         cp ${proteomes_omamerdb_inputhog[2]}/${proteomes_omamerdb_inputhog[0]}.hogmap  ${proteomes_omamerdb_inputhog[0]}.hogmap
     else
-        omamer search --db ${proteomes_omamerdb_inputhog[1]} --query ${proteomes_omamerdb_inputhog[0]} --nthreads 10  --out ${proteomes_omamerdb_inputhog[0]}.hogmap
+        omamer search --db ${proteomes_omamerdb_inputhog[1]} --query ${proteomes_omamerdb_inputhog[0]} --out ${proteomes_omamerdb_inputhog[0]}.hogmap
     fi
-  """
-
+  """  // --nthreads 10
 }
 
 
-process infer_roothogs{
-  publishDir  params.rhogs_folder // "${params.output_folder}/rhogs_all"
+process infer_roothogs{   // publishDir  params.rhogs_folder
   input:
-  val ready_omamer_run
-  path hogmap_folder
-  path proteome_folder
+    val ready_omamer_run
+    path hogmap_folder
+    path proteome_folder
   output:
-  path "*.fa"
-  path "gene_id_dic_xml.pickle"
-  val true     // ready_infer_roothogs   nextflow-io.github.io/patterns/state-dependency/
+    path "rhogs_all" // path "rhogs_all/*"
+    path "gene_id_dic_xml.pickle"
+    val true         // nextflow-io.github.io/patterns/state-dependency/
   script:
-  """
-   infer-roothogs  --logger-level DEBUG
-  """
+    """
+       infer-roothogs  --logger-level DEBUG
+    """
 }
 
-process batch_roothogs{
-  publishDir params.output_folder
+
+process batch_roothogs{ // publishDir params.output_folder
   input:
-  val ready_infer_roothogs
-  path rhogs_folder //"${params.output_folder}/rhogs_all"
+    val ready_infer_roothogs
+    //path rhogs_folder
+    path "rhogs_all"
   output:
-  path "rhogs_rest/*", optional: true
-  path "rhogs_big/*" , optional: true
-  val true
+    path "rhogs_rest/*", optional: true
+    path "rhogs_big/*" , optional: true
+    val true
   script:
-  """
-   batch-roothogs
-  """
+    """
+        batch-roothogs
+    """
 }
 
-process hog_big{
+process hog_big{ //publishDir params.pickles_rhogs_folder
   cpus  6
-  time {20.h}    // for very big rhog it might need more, or you could re-run and add `-resume`
-  memory {80.GB}
-
-  publishDir params.pickles_rhogs_folder
-
+  time {20.h}     // for very big rhog it might need more, or you could re-run and add `-resume`
+  memory {20.GB}
   input:
-  // val ready_batch_roothogs
-  // path rhogsbig_tree // = rhogsbig.combine(species_tree)
-  // rhogs_big_i  //"$rhogs_big/*.fa"
-  // path "species_tree.nwk"
-  val rhogsbig_tree_ready
+    val rhogsbig_tree_ready
   output:
-  path "*.pickle"
-
-  path "*.fa", optional: true   // msa         if write True
-  path "*.nwk", optional: true  // gene trees  if write True
-
-  val true
-  // path "pi_big_subhog/*"
-  // pi_big rhogs_big
-  // params.species_tree
-
+    path "pickle_rhogs/*.pickle"
+    // path "*.pickle"
+    path "*.fa", optional: true   // msa         if write True
+    path "*.nwk", optional: true  // gene trees  if write True
+    val true
   script:
-  """
-  infer-subhogs  --input-rhog-folder ${rhogsbig_tree_ready[0]} --species-tree ${rhogsbig_tree_ready[1]} --parallel --fragment-detection --low-so-detection
-  """
+    """
+        infer-subhogs  --input-rhog-folder ${rhogsbig_tree_ready[0]} --species-tree ${rhogsbig_tree_ready[1]} --parallel --fragment-detection --low-so-detection
+    """
 }
 
-
-process hog_rest{
-
-    publishDir params.pickles_rhogs_folder
-//   publishDir(
-//     path: {params.pickles_rhogs_folder},
-//     pattern: {"*.pickle"}
-//   )
-//   publishDir(
-//     path: {params.genetrees_folder},
-//     pattern: {"*.nwk"}
-//   )
-
+process hog_rest{ //publishDir params.pickles_rhogs_folder
   input:
-  // val ready_batch_roothogs
-  //path rhogsrest_tree // = rhogsrest.combine(species_tree)
-  val rhogsrest_tree_ready
-
+    val rhogsrest_tree_ready
   output:
-  path "*.pickle"
-
-  path "*.fa" , optional: true   // msa         if write True
-  path "*.nwk" , optional: true  // gene trees  if write True
-
-  val true
+    path "pickle_rhogs/*.pickle"
+    // path "*.pickle"
+    //path "pickle_rhogs/*.pickle"
+    path "*.fa" , optional: true   // msa         if write True
+    path "*.nwk" , optional: true  // gene trees  if write True
+    val true
   script:
-  """
-  infer-subhogs  --input-rhog-folder ${rhogsrest_tree_ready[0]}  --species-tree ${rhogsrest_tree_ready[1]} --fragment-detection --low-so-detection
-  """ // --parrallel False
+    """
+        infer-subhogs  --input-rhog-folder ${rhogsrest_tree_ready[0]}  --species-tree ${rhogsrest_tree_ready[1]} --fragment-detection --low-so-detection
+    """  // --parrallel False
 }
 
-process collect_subhogs{
 
+process collect_subhogs{
   memory {50.GB}
   publishDir params.output_folder, mode: 'copy'
   input:
-  val ready_hog_rest
-  val ready_hog_big
-  // path pickle_rhogs   // this is for depenedcy
-  path "pickle_rhogs" // this is the folder includes pickles_rhogs
-  path "gene_id_dic_xml.pickle"
-
+    val ready_hog_rest
+    val ready_hog_big     // path pickle_rhogs   // this is for depenedcy
+    path "pickle_rhogs/"  // "*.pickle"  // path "pickle_rhogs"   // this is the folder includes pickles_rhogs
+    path "gene_id_dic_xml.pickle"
+    path "rhogs_all"
   output:
-  path "output_hog_.orthoxml"
-
+    path "output_hog.orthoxml"
+    path "OrthologousGroupsFasta"
+    path "OrthologousGroups.tsv"
+    path "rootHOGs.tsv"
   script:
-  """
-   collect-subhogs
-  """
+    """
+        collect-subhogs
+    """
 }
 
 
-
 workflow {
     proteomes = Channel.fromPath(params.proteomes,  type:'any' ,checkIfExists:true)
     proteome_folder = Channel.fromPath(params.proteome_folder)
     hogmap_folder = Channel.fromPath(params.hogmap_folder)
-    rhogs_folder = Channel.fromPath(params.rhogs_folder)
+//    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}"}
+//    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)
-   // (hogmap, ready_omamer_run)= omamer_run(proteomes_omamerdb)
     ready_omamer_run_c = ready_omamer_run.collect()
-    // hogmaps.view{"hogmap ${it}"}
-
-    // proteome_folder.view{"proteome_folder ${it} "}
-    // (rhogs, gene_id_dic_xml) = infer_roothogs(hogmaps, hogmap_folder, proteome_folder)
-    (rhogs, gene_id_dic_xml, ready_infer_roothogs) = infer_roothogs(ready_omamer_run_c, hogmap_folder, proteome_folder)
-    // rhogs.view{"rhogs ${it}"}
-    // rhogs_folder.view{"rhogs_folder xx ${it}"}
 
+    (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()
+
     (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()
 
-   // ready_batch_roothogs_c.view{" ready_batch_roothogs_c 44  ${it}"}
-
     species_tree = Channel.fromPath(params.species_tree)
     rhogsbig = rhogs_big_list.flatten()
-    // rhogsbig.view{" rhogsbig ${it}"}
     rhogsbig_tree =  rhogsbig.combine(species_tree)
-    rhogsbig_tree_ready = rhogsbig_tree.combine(ready_batch_roothogs)
-    rhogsbig_tree_ready.view{"rhogsbig_tree_ready ${it}"}
+    rhogsbig_tree_ready = rhogsbig_tree.combine(ready_batch_roothogs)   //     rhogsbig_tree_ready.view{"rhogsbig_tree_ready ${it}"}
     (pickle_big_rhog, msas_out, genetrees_out, ready_hog_big) = hog_big(rhogsbig_tree_ready)
 
     rhogsrest = rhogs_rest_list.flatten()
-//     rhogsrest.view{" rhogs rest ${it}"}
     rhogsrest_tree =  rhogsrest.combine(species_tree)
-
-
     rhogsrest_tree_ready = rhogsrest_tree.combine(ready_batch_roothogs_c)
-//     rhogsrest_tree_ready.view{"rhogsrest_tree_ready ${it}"}
-
     (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")
 
-//     pickle_rest_rhog.flatten().view{" pickle_rest_rhog rest ${it}"}
-//     pickle_big_rhog.flatten().view{" pickle_big_rhog rest ${it}"}
-    prb = pickle_big_rhog.collect()
-    prr = pickle_rest_rhog.collect()
-    all_pickles = prb.mix(prr)
-//     gene_id_dic_xml = Channel.fromPath("gene_id_dic_xml.pickle")
-    pickle_rhogs_folder = Channel.fromPath(params.output_folder+"/pickle_rhogs")
-//     orthoxml_file = collect_subhogs(all_pickles.collect(), pickle_rhogs_folder, gene_id_dic_xml)
-
-    orthoxml_file = collect_subhogs(ready_hog_rest.collect(), ready_hog_big.collect(), pickles_rhogs_folder, gene_id_dic_xml)
+    (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}"}
 
-
-
 }
 
 // memory {12.GB * (2*task.attempt - 1)}
diff --git a/FastOMA/_config.py b/FastOMA/_config.py
index 7fc0a67..481080c 100644
--- a/FastOMA/_config.py
+++ b/FastOMA/_config.py
@@ -81,7 +81,11 @@
 
 # batch_roothogs
 big_rhog_filesize_thresh = 600 * 1000
-sum_list_rhogs_filesize_thresh = 2 * 1e6
+sum_list_rhogs_filesize_thresh = 1 * 1e5
+
+#big_rhog_filesize_thresh = 600 * 1000
+#sum_list_rhogs_filesize_thresh = 2 * 1e6
+
 
 # big_rhog_filesize_thresh = 1.6 * 1000  # 600 would be better
 # sum_list_rhogs_filesize_thresh = 5 * 1e3
diff --git a/README.md b/README.md
index 2d57677..45e9346 100644
--- a/README.md
+++ b/README.md
@@ -176,12 +176,12 @@ This means that if you remove the `work` folder, you will not have access to the
 If you are working on a large scale project, you may need to change the limitation on the number of files opened in linux using `ulimit -n 271072`. 
 
 ### using omamer's output
-The first step of the FastOMA pipele is to run [OMAmer](https://github.com/DessimozLab/omamer). If you already have the hogmap files, you can put them in the `in_folder/hogmap_input_folder`.
+The first step of the FastOMA pipele is to run [OMAmer](https://github.com/DessimozLab/omamer). If you already have the hogmap files, you can put them in the `in_folder/hogmap_in`.
 Then your structure of files will be 
 ```
 $ tree ../testdata/
 ├── in_folder
-│   ├── hogmap_input_folder
+│   ├── hogmap_in
 │   │   ├── CHLTR.fa.hogmap
 │   │   ├── MYCGE.fa.hogmap
 │   ├── omamerdb.h5