I am trying to define and execute a snakemake workflow in pure python using the snakemake python package. There isn’t a specific use case. I am just trying to understand what is possible and what is not in snakemake. I imagine something like

I am trying to define and execute a snakemake workflow in pure python using the snakemake python package. There isn’t a specific use case. I am just trying to understand what is possible and what is not in snakemake. I imagine something like

I am trying to define and execute a snakemake workflow in pure python using the snakemake python package. There isn’t a specific use case. I am just trying to understand what is possible and what is not in snakemake. I imagine something like

I am trying to define and execute a snakemake workflow in pure python using the snakemake python package. There isn’t a specific use case. I am just trying to understand what is possible and what is not in snakemake. I imagine something like

I have a workflow which performs a number of QC tasks on the content of a directory. Therefore, this directory is the only input and I invoke as follows:

I have a workflow which performs a number of QC tasks on the content of a directory. Therefore, this directory is the only input and I invoke as follows:

I have a snakemake pipeline that runs a genetic analysis. The genome has been split into many ‘regions’. These regions can run in parallel, and therefore I’ve used expand(), and they all run as expected.

Snakemake version : 7.32.4,
python version : 3.10.14,
linux ubuntu system

I have a project that was running fine until I had to update the conda environment. Suddenly, certain strings got extra spaces around variables that are inserted in the string with f"...".

I’m writing a Snakemake pipeline to run some simulations. The key points are that:
(1) I run simulations across a space of values of parameters A, B & C and in n replicates,
(2) I plot the results averaged across the replicates for each parameter combination,
(3) I want to combine the plots so that, for each combination of B & C, I produce a plot with panels for different values of A.