Commit 1fa2d519 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

Merge branch 'feature-s/fix-grep-reads' into 'dev'

grep-reads needs to have clone files produced

See merge request !973
parents 8de97110 dde9a9a6
Pipeline #256737 passed with stages
in 83 minutes and 56 seconds
......@@ -252,8 +252,8 @@ def run_vidjil(id_file, id_config, id_data, grep_reads,
cmd = defs.DIR_VIDJIL + '/vidjil-algo '
if grep_reads:
# TODO: security, assert grep_reads XXXX
vidjil_cmd += ' --grep-reads "%s" ' % grep_reads
if re.match(r"^[acgtnACGTN]+$", grep_reads):
vidjil_cmd += ' --out-clone-files --grep-reads "%s" ' % grep_reads
os.makedirs(out_folder)
out_log = out_folder+'/'+output_filename+'.vidjil.log'
......
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