diff --git a/gen_lp.py b/gen_lp.py
deleted file mode 100644
index 7d10957..0000000
--- a/gen_lp.py
+++ /dev/null
@@ -1,31 +0,0 @@
-"""Script to generate lp file from OSeMOSYS datafile, within a workflow and to provide output in case not possible avoiding breaking of the workflow.
-"""
-import os
-import sys
-import subprocess as sp
-
-def gen_lp(p_df: str, p_lp: str):
-
-    str_cmd = "glpsol -m "+os.path.join('"model','osemosys.txt"') + ' -d "%(data)s" --wlp "%(lp)s" --check' % {'data': p_df, 'lp': p_lp}
-    
-    try:
-        sp.run(str_cmd, shell=True, capture_output=True)
-    except:
-        file_error = open(os.sep.join(p_lp.split('/')[:-1]+['lp-error.txt']), "w")
-        file_error.close()
-
-if __name__ == "__main__":
-    
-    args = sys.argv[1:]
-
-    if len(args) != 2:
-        print("Usage: python gen_lp.py <path_df> <path_lp>")
-        exit(1)
-    
-    path_df = args[0]
-    path_lp = args[1]
-
-    gen_lp(path_df, path_lp)
-
-    file_done = open(os.sep.join(path_lp.split('/')[:-1]+['lp_done.txt']), "w")
-    file_done.close()
\ No newline at end of file
diff --git a/snakefile b/snakefile
index c3c7599..0690c0c 100644
--- a/snakefile
+++ b/snakefile
@@ -1,17 +1,22 @@
 import os
+import pandas as pd
 
-scenario_path = os.path.join("input_data", "diagnostic_scen")
-SCENARIOS = [x.path for x in os.scandir(scenario_path) if x.is_dir()]
+dp_files = pd.read_csv('config/dp_files.txt')
+
+scenario_path = os.path.join("input_data")
+SCENARIOS = [x.name for x in os.scandir(scenario_path) if x.is_dir()]
 
 rule all:
     input:
-        expand("results/{scen}/{scen}.xlsx", scen=SCENARIOS) #for testing, to be changed during development
+        expand("results/{scen}.xlsx", scen=SCENARIOS) #for testing, to be changed during development
 
 rule convert_dp:
+    message: "Coverting datapackage for {wildcards.scen}"
     input:
-        dp_path = "{scen}/datapackage.json"
+        other = expand("input_data/{{scen}}/{files}", files=dp_files),
+        dp_path = "input_data/{scen}/datapackage.json"
     output:
-        df_path = "{scen}/{scen}.txt"
+        df_path = "working_directory/{scen}.txt"
     conda:
         "envs/otoole_env.yaml"
     shell:
@@ -21,7 +26,7 @@ rule pre_process:
     input:
         "working_directory/{scen}.txt"
     output:
-        temporary("working_directory/{scen}.pre")
+        temp("working_directory/{scen}.pre")
     conda:
         "envs/otoole_env.yaml"
     shell:
@@ -29,47 +34,48 @@ rule pre_process:
 
 rule build_lp:
     input:
-        df_path = "{scen}/{scen}.txt"
+        df_path = "working_directory/{scen}.pre"
     params:
-        model_path = "model/osemosys.txt",
-        lp_path = "{scen}/{scen}.lp"
+        model_path = "model/osemosys.txt"
     output:
-        lp_complete_path = "{scen}/lp_done.txt"
+        temp("working_directory/{scen}.lp")
+    log:
+        "working_directory/{scen}.log"
     shell:
-        "python gen_lp.py {input.df_path} {params.lp_path}"
+        "glpsol -m {params.model_path} -d {input.df_path} --wlp {output} --check > {log}"
 
 rule run_model:
+    message: "Solving the LP for '{input}'"
     input:
-        lp_complete_path = "{scen}/lp_done.txt"
-    params:
-        lp_path = "{scen}/{scen}.lp",
-        path = "results/{scen}/{scen}"
+        "working_directory/{scen}.lp",
     output:
-        done_path = "results/{scen}/{scen}-sol_done.txt"
+         temp("working_directory/{scen}.sol")
     conda:
         "envs/gurobi_env.yaml"
-    shell:
-        "python run.py {params.lp_path} {params.path}"
+    log:
+        "working_directory/gurobi/{scen}.log",
+    threads: 2
+    script:
+        "run.py"
 
 rule convert_sol:
     input:
-        sol_complete_path = "results/{scen}/{scen}-sol_done.txt",
-        dp_path = "{scen}/datapackage.json"
+        sol_path = "working_directory/{scen}.sol",
+        dp_path = "input_data/{scen}/datapackage.json"
     params:
-        sol_path = "results/{scen}/{scen}.sol",
         res_folder = "results/{scen}/results_csv"
     output:
         res_path = "results/{scen}/res-csv_done.txt"
     conda:
         "envs/otoole_env.yaml"
     shell:
-        "python convert.py {params.sol_path} {params.res_folder} {input.dp_path}"
+        "python convert.py {input.sol_path} {params.res_folder} {input.dp_path}"
 
 rule create_configs:
     input:
         config_tmpl = "config.yaml"
     output:
-        config_scen = "config_{scen}.yaml"
+        config_scen = "working_directory/config_{scen}.yaml"
     conda:
         "envs/yaml_env.yaml"
     shell:
@@ -78,12 +84,12 @@ rule create_configs:
 rule res_to_iamc:
     input:
         res_path = "results/{scen}/res-csv_done.txt",
-        config_file = "config_{scen}.yaml"
+        config_file = "working_directory/config_{scen}.yaml"
     params:
-        inputs_folder = "{scen}/data",
+        inputs_folder = "input_data/{scen}/data",
         res_folder = "results/{scen}/results_csv"
     output:
-        output_file = "results/{scen}/{scen}.xlsx"
+        output_file = "results/{scen}.xlsx"
     conda:
         "envs/openentrance_env.yaml"
     shell: