Generalize file param input for python scripts

workflow/scripts/modifyFetch.py

@@ -6,20 +6,20 @@ import re
 
 def get_args():
     parser = argparse.ArgumentParser()
-    parser.add_argument('-f', '--fetchFile',help="The fetch file from bdgap.zip.",required=True)
+    parser.add_argument('-f', '--files',help="The fetch file from bdgap.zip.",required=True)
     args = parser.parse_args()
     return args
 
 def main():
     args = get_args()
-    fetchFile = pd.read_csv(args.fetchFile+"/fetch.txt",sep="\t",header=None)
-    fileFile = pd.read_csv(args.fetchFile+"/data/File.csv",sep=",",header=0)
+    fetchFile = pd.read_csv(args.files+"/fetch.txt",sep="\t",header=None)
+    fileFile = pd.read_csv(args.files+"/data/File.csv",sep=",",header=0)
     fileFile_filtered = fileFile[fileFile["File_Type"]=="FastQ"]
     fetchFile_filtered = fetchFile[fetchFile[2].str[-9:]==".fastq.gz"]
     fetchFile_filtered_renamed = fetchFile_filtered
     for i in fileFile_filtered["File_Name"]:
         fetchFile_filtered_renamed[2][fetchFile_filtered_renamed[2].str.contains(i,regex=False)] = fetchFile_filtered_renamed[2][fetchFile_filtered_renamed[2].str.contains(i,regex=False)].values[0].replace(re.sub("\.R.\.fastq\.gz","",i),fileFile_filtered["Replicate_RID"][fileFile_filtered["File_Name"]==i].values[0])
-    fetchFile_filtered_renamed.to_csv(args.fetchFile+"/fetch.txt",sep="\t",header=False,index=False)
+    fetchFile_filtered_renamed.to_csv(args.files+"/fetch.txt",sep="\t",header=False,index=False)
 
 if __name__ == '__main__':
     main()
\ No newline at end of file

workflow/scripts/splitFetch.py

@@ -6,14 +6,14 @@ import os
 
 def get_args():
     parser = argparse.ArgumentParser()
-    parser.add_argument('-f', '--fetchFile',help="The fetch file from bdgap.zip.",required=True)
+    parser.add_argument('-f', '--files',help="The fetch file from bdgap.zip.",required=True)
     args = parser.parse_args()
     return args
 
 def main():
     args = get_args()
-    fetchFile = pd.read_csv(args.fetchFile+"/fetch.txt",sep="\t",header=None)
-    fileFile = pd.read_csv(args.fetchFile+"/data/File.csv",sep=",",header=0)
+    fetchFile = pd.read_csv(args.files+"/fetch.txt",sep="\t",header=None)
+    fileFile = pd.read_csv(args.files+"/data/File.csv",sep=",",header=0)
     replicateRID = fileFile.Replicate_RID.unique()
     fetchArray = {i:fileFile.URI[(fileFile.Replicate_RID == i) & (fileFile.File_Type == "FastQ")] for i in replicateRID}
     for i in replicateRID: