Commit 2958f7c0 authored by HERBERT Ryan's avatar HERBERT Ryan

task.py added fuse

parent e99363a7
...@@ -200,7 +200,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse, grep_reads, ...@@ -200,7 +200,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse, grep_reads,
return "SUCCESS" return "SUCCESS"
def run_mixcr(id_file, id_config, id_data, clean_before=False, clean_after=False): def run_mixcr(id_file, id_config, id_data, id_fuse, clean_before=False, clean_after=False):
from subprocess import Popen, PIPE, STDOUT, os from subprocess import Popen, PIPE, STDOUT, os
import time import time
...@@ -266,6 +266,12 @@ def run_mixcr(id_file, id_config, id_data, clean_before=False, clean_after=False ...@@ -266,6 +266,12 @@ def run_mixcr(id_file, id_config, id_data, clean_before=False, clean_after=False
res = {"message": "[%s] c%s: MiXCR finished - %s" % (id_data, id_config, out_folder)} res = {"message": "[%s] c%s: MiXCR finished - %s" % (id_data, id_config, out_folder)}
log.info(res) log.info(res)
for row in db(db.sample_set_membership.sequence_file_id==id_file).select() :
sample_set_id = row.sample_set_id
print row.sample_set_id
run_fuse(id_file, id_config, id_data, id_fuse, sample_set_id, clean_before = False)
return "SUCCESS" return "SUCCESS"
def run_copy(id_file, id_config, id_data, id_fuse, clean_before=False, clean_after=False): def run_copy(id_file, id_config, id_data, id_fuse, clean_before=False, clean_after=False):
......
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