Update megahit input functions

generate_workflow.py

@@ -398,15 +398,13 @@ def generate_pipeline_files(workflow_name, output_dir, local_config="default"):
 
     ### Copy scripts and other files
 
-    NB_SCRIPTS = len(list(generate_prepare_report_scripts())) + len(list(generate_tools_scripts()))
+    NB_SCRIPTS = len(list(generate_prepare_report_scripts()["SCRIPTS"])) + len(list(generate_tools_scripts()))
 
     if not os.path.isdir(output_dir + "/files/scripts"):
         os.mkdir(output_dir + "/files/scripts")
     if (NB_SCRIPTS==0):
         with open(output_dir + "/files/scripts/.gitignore",'w') as gitignore:
-            to_write ="""# Ignore everything in this directory
-*
-# Except this file
+            to_write ="""# gitignore to force creation of scripts dir
 !.gitignore
 """
             gitignore.write(to_write)

generate_workflow_snakefile.py

@@ -18,32 +18,7 @@ def generate(name):
 
     # imports
 
-    result += "import os\n"
-    result += "import re\n"
-    result += "import snakemake.utils\n"
-    result += "import csv\n"
-
-    result += "\n"
-
-    # Wildcards
-
-    result += "#############\n"
-    result += "# Wildcards #\n"
-    result += "#############\n"
-
-    result += "\n"
-
-    #result += "SAMPLES = config[\"samples\"]\n"
-    result += "STEPS = config[\"steps\"]\n"
-    result += "PREPARE_REPORT_OUTPUTS = config[\"prepare_report_outputs\"]\n"
-    result += "PREPARE_REPORT_SCRIPTS = config[\"prepare_report_scripts\"]\n"
-    result += "OUTPUTS = config[\"outputs\"]\n"
-    result += "PARAMS_INFO = config[\"params_info\"]\n"
-    if ("stop_cases" in yaml.keys()):
-        result += "STOP_CASES = config[\"stop_cases\"]\n"
-    result += "config = config[\"params\"]\n"
-
-    result += "\n"
+    result += "{import global_imports}\n\n"
 
     # intputs
 

workflows/Mito_Assembler_Megahit/Mito_Assembler_Megahit.snakefile

@@ -22,11 +22,15 @@ def quality_check__fastqc_PE_inputs():
 	inputs["read2"] = raw_reads["read2"]
 	return inputs
 
-def assembling__megahit_inputs():
+def assembling__megahit_SE_inputs():
     inputs = dict()
     inputs["read"] = expand(raw_reads["read"],sample=SAMPLES)
-    if (config["SeOrPe"] == "PE"):
-        inputs["read2"] = expand(raw_reads["read2"],sample=SAMPLES)
+    return inputs
+
+def assembling__megahit_PE_inputs():
+    inputs = dict()
+    inputs["read"] = expand(raw_reads["read"],sample=SAMPLES)
+    inputs["read2"] = expand(raw_reads["read2"],sample=SAMPLES)
     return inputs
 
 def find_mitoscaf__mitoz_findmitoscaf_inputs():

workflows/Virus_Assembler_Megahit/Virus_Assembler_Megahit.snakefile

@@ -22,11 +22,15 @@ def fastqc_PE_inputs():
 	inputs["read2"] = raw_reads["read2"]
 	return inputs
 
-def megahit_inputs():
+def assembling__megahit_SE_inputs():
     inputs = dict()
     inputs["read"] = expand(raw_reads["read"],sample=SAMPLES)
-    if (config["SeOrPe"] == "PE"):
-        inputs["read2"] = expand(raw_reads["read2"],sample=SAMPLES)
+    return inputs
+
+def assembling__megahit_PE_inputs():
+    inputs = dict()
+    inputs["read"] = expand(raw_reads["read"],sample=SAMPLES)
+    inputs["read2"] = expand(raw_reads["read2"],sample=SAMPLES)
     return inputs
 
 def blast_refseq_inputs():