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Bug in 7.32.4 trying to access outputs with the rules object: 'Namedlist' object has no attribute <x> #2481

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nickp60 opened this issue Oct 13, 2023 · 2 comments
Open

Bug in 7.32.4 trying to access outputs with the rules object: 'Namedlist' object has no attribute <x> #2481

nickp60 opened this issue Oct 13, 2023 · 2 comments
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@nickp60
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nickp60 commented Oct 13, 2023

Snakemake version
I experience this bug with snakemake 7.32.4, but not with 7.31.1 or prior versions. The versions in between (7.32.0, 7.32.1, etc) appear to have unrelated bugs that have been addressed elsewhere.

Describe the bug
I am having errors in a pipeline we run routinely that we have tracked down to recent changes to how snakemake allows access to the rules object. The error I get is as follows:

AttributeError in file $HOME/GitHub/vdblab-shotgun/workflow/rules/hostdeplete.smk, line 163:
'Namedlist' object has no attribute 'bam'
  File "/lila/home/watersn/GitHub/vdblab-shotgun/workflow/Snakefile", line 70, in <module>
  File "/lila/home/watersn/GitHub/vdblab-shotgun/workflow/rules/preprocess.smk", line 259, in <module>
  File "/lila/home/watersn/GitHub/vdblab-shotgun/workflow/rules/hostdeplete.smk", line 163, in <module>

The workflow module in questions is here: https://github.com/vdblab/vdblab-shotgun/blob/main/workflow/rules/hostdeplete.smk

Additional context
This appears to be related to changes introduced here: #2404
@nickp60 nickp60 added the bug Something isn't working label Oct 13, 2023
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nickp60 commented Jan 17, 2024

This persists in 8.2.0

nickp60 added a commit to vdblab/vdblab-shotgun that referenced this issue Jan 17, 2024
@nickp60
simplify host deplete imports to avoid weird errors
ad20cfd 
Issues like snakemake/snakemake#2481 persisted in 8.2.0, and it
appears to be resolved after I simplified these imports.  previously, the Snakefile used the
preprocess module which used the hostdeplete module which used the snap and bowtie2 modules.
I moved the code from the snap and bowtie2 modules into the hostdeplete one, and many
strange errors went away.
@nickp60
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nickp60 commented Jan 17, 2024

I was able to get around this by simplifying the import structure of the workflow. It seems like 4 levels of imports was too much for snakemake :/ , as consolidating snakefiles to 3 levels of imports resolved the issue.

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