Small suggestions #29
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snakemake doesn't like when you mess with it while running it. I get the following error when removing .snakemake while running snakemake itself:
````
Complete log(s): /Users/cr/code/rubella/ingest/.snakemake/log/2025-05-05T203735.022933.snakemake.log
Exception in thread Thread-1 (_monitor):
Traceback (most recent call last):
File "/Users/cr/micromamba/envs/py12/lib/python3.12/threading.py", line 1075, in _bootstrap_inner
self.run()
File "/Users/cr/micromamba/envs/py12/lib/python3.12/threading.py", line 1012, in run
self._target(*self._args, **self._kwargs)
File "/Users/cr/micromamba/envs/py12/lib/python3.12/logging/handlers.py", line 1598, in _monitor
self.handle(record)
File "/Users/cr/micromamba/envs/py12/lib/python3.12/logging/handlers.py", line 1579, in handle
handler.handle(record)
File "/Users/cr/micromamba/envs/py12/lib/python3.12/logging/__init__.py", line 1028, in handle
self.emit(record)
File "/Users/cr/micromamba/envs/py12/lib/python3.12/logging/__init__.py", line 1278, in emit
self.stream = self._open()
^^^^^^^^^^^^
File "/Users/cr/micromamba/envs/py12/lib/python3.12/logging/__init__.py", line 1263, in _open
return open_func(self.baseFilename, self.mode,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/Users/cr/code/rubella/ingest/.snakemake/log/2025-05-05T203735.022933.snakemake.log'
```
It's annoying that one needs to manually add this file but it allows: `snakemake` as opposed to having to type `snakemake -c1 --ri --printshellcmds`
First thing I look for :)
resolves #28 Trailing `|` was interpreted as "or anything" which ends up always being true
Contributor
|
Please note, the rubella build is still under active development. |
tsibley
reviewed
May 6, 2025
ingest/profiles/default/config.yaml
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| cores: all | ||
| printshellcmds: true | ||
| ri: true No newline at end of file |
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Do you know you can make these your global default by putting the profile somewhere shared and setting SNAKEMAKE_PROFILE, e.g.
export SNAKEMAKE_PROFILE=~/.config/snakemake/default
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It's been a while since I've looked at a Nextstrain workflow other than mpox so thought I go through this one and make some suggestions as I review the code
Commits can be cherry-picked, there's no single theme