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As you can see, the environment variables are quoted as a group which makes bash crash.
The issue seems to be the usage of AlwaysQuotedFormatter in snakemake.utils when calling format for the job script with _quote_all=True. Changing this to _quote_all=False fixed the issue for me, but I am not sure if this breaks other cases.
The text was updated successfully, but these errors were encountered:
This seems to be loosely connected to #1007 in that it also involves quoting of environment variables (see also #1008). Rather than disabling _quote_all entirely I have circumvented this by manually prepending envvars to exec_job rather than letting format_job() handle it in
First of all, sorry for the late response. After many new features, Snakemake is approaching feature completeness (at least for my personal agenda and at the moment). Hence, now is the time to fix or close all the open bugs.
Above PR provides a fix on a kind of global scale. Thanks a lot for pointing to the issue!