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Protects against spaces in env vars and avoid quoting of all env vars as single entity #1008

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Protects against spaces in env vars and avoid quoting of all env vars as single entity #1008

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Protects against spaces in env vars and avoid quoting of all env vars…
pcm32 May 21, 2021
50c0a42
Corrects comments
pcm32 May 21, 2021
9239c59
Black based reformatting.
pcm32 Jun 14, 2021
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6 changes: 4 additions & 2 deletions snakemake/executors/__init__.py
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Expand Up @@ -792,13 +792,15 @@ def write_jobscript(self, job, jobscript, **kwargs):
use_threads = "--force-use-threads" if not job.is_group() else ""

envvars = " ".join(
"{}={}".format(var, os.environ[var]) for var in self.workflow.envvars
# quotes values, as envvars values could have spaces
"{}='{}'".format(var, os.environ[var])
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What if the env var itself contains single quotes? Python provides escape mechanisms that should be used instead: use repr(os.environ[var]).

for var in self.workflow.envvars
)

exec_job = self.format_job(
self.exec_job,
job,
_quote_all=True,
_quote_all=False,
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Are you sure this has to be deactivated? It is also needed for other things in the exec job template.

use_threads=use_threads,
envvars=envvars,
**kwargs,
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