add a parsing step after diffsel

lib/convergence_detection.ml

@@ -37,22 +37,31 @@ let diffsel ~(phy_n:nucleotide_phylip workflow) ~(tree: _ workflow) ~(w_every:in
         opt "-ncond"  int 2 ;
         opt "-x" seq [ int w_every; string " "; int n_cycles];
         ident chainname ;
-    ]
+    ];
   ] in
   let package = tmp // "diffsel_script_utils.py" in
   let script = tmp // "diffsel_analyze_result.py" in
+  let chainname = (dep run_diffsel) // "myrun" in
+  let out = dest // "diffsel_results.tsv" in
   workflow ~descr:"convergence_detection.parse_diffsel" [
     docker env (
       and_list [
+        mkdir_p dest ;
+        mkdir_p tmp ;
+        cd tmp ;
+        cmd "ls" [dep run_diffsel];
+        cmd "ls" [dep phy_n]; (* required dep to link the file in the env *)
+        cmd "ls" [dep tree]; (* required dep to link the file in the env *)
+
         (*python diffsel_analyze_result.py [-r /path/to/readdiffsel] [-o output_file] chainname *)
-        cmd "cat" ~stdout:package [ file_dump (string Scripts.diffsel_analyze_result) ] ;
+        cmd "cat" ~stdout:package [ file_dump (string Scripts.diffsel_script_utils) ] ;
         cmd "cat" ~stdout:script [ file_dump (string Scripts.diffsel_analyze_result) ] ;
-        cd tmp ;
+
         cmd "python" [
           string "diffsel_analyze_result.py" ;
-          opt "-r" string "_build/readdiffsel" ;
-          opt "-o" ident dest ;
-          dep (run_diffsel / selector ["myrun.chain"])
+          opt "-r" string "/diffsel/_build/readdiffsel" ;
+          opt "-o" ident out ;
+          ident chainname ;
         ]
       ]
     )