Commit 1ed6822d authored by khalid's avatar khalid
Browse files

EdgeR and deseq2 use an expandable input

parent 4ad900d6
...@@ -141,10 +141,9 @@ def generate(name, path_yaml = "", path_input = DEFAULT_PATH_INPUT, path_output ...@@ -141,10 +141,9 @@ def generate(name, path_yaml = "", path_input = DEFAULT_PATH_INPUT, path_output
#if not param["origin_command"] in raw_inputs: #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" # result += "\tinputs[\"" + param["input_name"] + "\"].append(" + expand_begin + param["origin_command"] + "[\"" + param["origin_name"] + "\"]" + expand_end + ")\n"
# raw_inputs.append(param["origin_command"]) # raw_inputs.append(param["origin_command"])
reslt += "n" reslt += "\n"
else: 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" 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 # Inputs de type liste
elif ("list" in INPUT_YAML and INPUT_YAML["list"]): elif ("list" in INPUT_YAML and INPUT_YAML["list"]):
if param["input_name"] not in inputs_list_from_yaml: if param["input_name"] not in inputs_list_from_yaml:
......
...@@ -18,7 +18,7 @@ ...@@ -18,7 +18,7 @@
output_dir: deseq2, output_dir: deseq2,
inputs: 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"}, { name: popmap_file, type: "popmap", file: "", description: "Path to tsv file with samples conditions"},
], ],
outputs: outputs:
......
...@@ -17,7 +17,7 @@ ...@@ -17,7 +17,7 @@
output_dir: edger, output_dir: edger,
inputs: 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"}, { name: group_file, type: "popmap", file: "", description: "Path to tsv file with samples conditions"},
], ],
outputs: outputs:
......
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