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Tag: snakemake

Snakemake doesn’t activate conda environment correctly

I have a Python module modulename installed in a conda environment called myenvname. My snakemake file consists of one simple rule: The contents of the test2.py are the following: When I run the above snakemake file with the command snakemake -j 1 –use-conda –conda-frontend conda I get ModuleNotFoundError, which would imply that there is no modulename in my specified environment.

Is there a function in snakemake to make the list of output dependent on the arguments passed into the shell command

I have a snakemake rule that calls a python program, the output of the python program is dependent on the arguments passed. I would like to make snakemake aware of the differences between the expected output when a certain parameter is passed (Boolean) or not passed. My current solution is to create a list of output list_phen_gen_output dependent on the

Wrong snakemake glob_wilcards and wildcard_constraints

Within my snakemake pipeline I’m trying to retrieve the correct wildcards. I’ve looked into wildcard_constraints and this post and this post, however I can’t figure out the exact solution. Here’s an example of file names within 2 datasets. 1 dataset contains paired mouse RNAseq read files and another dataset contains human paired RNAseq read files. “Mus_musculus” dataset is “PRJNA362883_GSE93946_SRP097621” with

snakemake – accessing config variables from cluster submission wrapper

I am using a cluster submission wrapper script with snakemake –cluster “python qsub_script.py”. I need to pass a global variable, taken from the config[‘someVar’]. This should be applied to all rules. I could add it to the params of each rule, and then access it using job_properties[‘params’][‘someVar’], but this is probably not the best solution. Is there a way to

Use local directory for wrapper in Snakemake rule

I want to know how to use a local directory for wrapper in Snakemake rule. I have read this Use Github URL for wrapper in Snakemake rule and try follows command But, I get a stderr with ‘NoneType’ object has no attribute ‘name’. Any help is much appreciated. Thanks. AdvertisementAnswer It is (slightly hidden) mentioned […]

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