Debug multiple mito circos generation

Mito_Assembler_Megahit/files/Snakefile

@@ -3,8 +3,6 @@ import re
 import snakemake.utils
 import csv
 
-dir_path = "/workflow"
-
 #############
 # Wildcards #
 #############
@@ -308,6 +306,8 @@ rule mitoz_annotate_SE:
         "then \n"
         "   for mito in $(grep \"mt[0-9]\{{1,\}}\" circos.dep | cut -f 1 | uniq) \n"
         "   do \n"
+        "   cd {params.circos_dir} && "
+        "   echo \"Treating mito $mito\" && "
         "   sed \"s/circos/circos$mito/g\" circos.conf > circos$mito.conf && "
         "   grep $mito circos.depth.txt > circos$mito.depth.txt && "
         "   grep $mito circos.karyotype.txt > circos$mito.karyotype.txt && "
@@ -355,6 +355,8 @@ rule mitoz_annotate_PE:
         "then \n"
         "   for mito in $(grep \"mt[0-9]\{{1,\}}\" circos.dep | cut -f 1 | uniq) \n"
         "   do \n"
+        "   cd {params.circos_dir} && "
+        "   echo \"Treating mito $mito\" && "
         "   sed \"s/circos/circos$mito/g\" circos.conf > circos$mito.conf && "
         "   grep $mito circos.depth.txt > circos$mito.depth.txt && "
         "   grep $mito circos.karyotype.txt > circos$mito.karyotype.txt && "

Mito_Assembler_Megahit/files/get_samples.py

@@ -35,8 +35,8 @@ def main():
     if len(sys.argv) == 3:
         print(sample_list(sys.argv[1],sys.argv[2]))
     else:
-        exit("""Need two parameters: workflow name, output dir, (local_config)
-Usage: ./generate_workflow.py workflow_name output_dir (local_config)""")
+        exit("""Needs 2 arguments: reads_directory, SeOrPe
+Usage: ./get_samples.py reads_directory SeOrPe""")
 
 if __name__ == "__main__":
     # execute only if run as a script