Commit a9892948 authored by Vidjil CI's avatar Vidjil CI Committed by Mathieu Giraud

models/task.py: translate 'next' configs into runs within VIDJIL_NEXT_DIR

See vdj#603.
parent 06bb97f4
Pipeline #16735 passed with stages
in 25 seconds
......@@ -173,7 +173,6 @@ def run_vidjil(id_file, id_config, id_data, grep_reads,
return "FAIL"
## les chemins d'acces a vidjil / aux fichiers de sequences
germline_folder = defs.DIR_GERMLINE
upload_folder = defs.DIR_SEQUENCES
out_folder = defs.DIR_OUT_VIDJIL_ID % id_data
......@@ -189,7 +188,14 @@ def run_vidjil(id_file, id_config, id_data, grep_reads,
## config de vidjil
vidjil_cmd = db.config[id_config].command
vidjil_cmd = vidjil_cmd.replace( ' germline' ,germline_folder)
if 'next' in vidjil_cmd:
vidjil_cmd = vidjil_cmd.replace('next', '')
vidjil_cmd = vidjil_cmd.replace(' germline' , defs.DIR_GERMLINE_NEXT)
cmd = defs.DIR_VIDJIL_NEXT + '/vidjil-algo '
else:
vidjil_cmd = vidjil_cmd.replace(' germline' , defs.DIR_GERMLINE)
cmd = defs.DIR_VIDJIL + '/vidjil '
if grep_reads:
# TODO: security, assert grep_reads XXXX
......@@ -201,7 +207,7 @@ def run_vidjil(id_file, id_config, id_data, grep_reads,
try:
## commande complete
cmd = defs.DIR_VIDJIL + '/vidjil ' + ' -o ' + out_folder + " -b " + output_filename
cmd += ' -o ' + out_folder + " -b " + output_filename
cmd += ' ' + vidjil_cmd + ' '+ seq_file
## execute la commande vidjil
......
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