EdgeR and deseq2 use an expandable input

generate_workflow_snakefile.py

@@ -141,10 +141,9 @@ def generate(name, path_yaml = "", path_input = DEFAULT_PATH_INPUT, path_output
                                 #if not param["origin_command"] in raw_inputs:
                                 #   result += "\tinputs[\"" + param["input_name"] + "\"].append(" + expand_begin + param["origin_command"] + "[\"" + param["origin_name"] + "\"]" + expand_end + ")\n"
                                 #   raw_inputs.append(param["origin_command"])
-                                reslt += "n"
+                                reslt += "\n"
                             else:
                                 result += "\tinputs[\"" + param["input_name"] + "\"] = expand(" + expand_begin + "rules." + param["origin_step"] + "__" + param["origin_command"] + ".output." + param["origin_name"] + expand_end + ", sample=SAMPLES)\n"
-
                         # Inputs de type liste
                         elif ("list" in INPUT_YAML and INPUT_YAML["list"]):
                             if param["input_name"] not in inputs_list_from_yaml:

tools/deseq2/deseq2.yaml

@@ -18,7 +18,7 @@
         output_dir: deseq2,
         inputs: 
           [
-            { name: counts, type: "tsv" },
+            { name: counts, type: "tsv", expand: true }, #will expand over counts for samples in SAMPLES
             { name: popmap_file, type: "popmap", file: "", description: "Path to tsv file with samples conditions"},
           ],
         outputs:

tools/edger/edger.yaml

@@ -17,7 +17,7 @@
         output_dir: edger,
         inputs: 
           [
-            { name: counts, type: "tsv" },
+            { name: counts, type: "tsv" , expand: true}, #will expand over counts for samples in SAMPLES
             { name: group_file, type: "popmap", file: "", description: "Path to tsv file with samples conditions"},
           ],
         outputs: