Commit 5dc21501 authored by Mikaël Salson's avatar Mikaël Salson Committed by Vidjil Team

models/taks.py: replace germline with the germline_folder.

In some configs we don't have the trailing slash at the end of germline.
But we ensure we have a space before germline (not to match too many things).
Are we sure that we necessarily have a space before?
parent 1d60231d
...@@ -83,7 +83,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse, clean_before=False, clean_a ...@@ -83,7 +83,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse, clean_before=False, clean_a
## config de vidjil ## config de vidjil
vidjil_cmd = db.config[id_config].command vidjil_cmd = db.config[id_config].command
vidjil_cmd = vidjil_cmd.replace( 'germline/' ,germline_folder) vidjil_cmd = vidjil_cmd.replace( ' germline' ,germline_folder)
os.makedirs(out_folder) os.makedirs(out_folder)
out_log = out_folder+'/'+output_filename+'.vidjil.log' out_log = out_folder+'/'+output_filename+'.vidjil.log'
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment