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redirect stderr #689

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redirect stderr #689

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1893d58
redirect stderr
siebrenf Apr 23, 2021
6ec2522
Merge branch 'develop' into redirect-stderr
Maarten-vd-Sande Apr 28, 2021
e4acfe0
Merge branch 'develop' into redirect-stderr
siebrenf May 3, 2021
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3 changes: 2 additions & 1 deletion seq2science/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -365,7 +365,8 @@ def _run(args, base_dir, workflows_dir, config_path):
parsed_args["config"]["no_config_log"] = True

# 5. start the "real" run where jobs actually get started
exit_code = snakemake.snakemake(**parsed_args)
with contextlib.redirect_stderr(sys.stdout):
exit_code = snakemake.snakemake(**parsed_args)
sys.exit(0) if exit_code else sys.exit(1)


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