Davide Corso

Hi, My jupyter notebook shows a vector output style separated by dots, which is different from the classic R output. For example, my notebook shows something like this ```r a...

Error on basilisk env for spatialDE wrapper

18

Hi @LTLA , I'm not sure if this is an error of basilisk, but it happened when the basilisk environment is created to run functions. Specifically, recently the Linux build...

Using an external conda environment with `run` for complex rules

12

**Snakemake version** 7.21.0 **Describe the bug** Hi, I have the following rule which contains both Python code and shell commands. ```python rule run_mags_prodigal: input: mags_folder=expand("{wdir}/{sample}/{mags_retrieval}", mags_retrieval=config["mags_retrieval"], allow_missing=True), output: directory("{wdir}/{sample}/mags_prodigal") params:...

Stop workflow (without error) if an output file is empty

1

Hi, is it possible to stop the snakemake workflow if an output file is empty? I've tried with the checkpoints but couldn't properly create the rules and make it work....

How to read Snakefile in Python and access to rules information

2

Hi, Does someone know if it is possible to read a Snakefile in Python and load all the rules into variables? For example, given the following Snakefile ``` WDIR="test" rule...

Using args_oap for quantification with general custom database

1

Hi, Thanks for providing this tool, I'm using it, and it is very fast and flexible in usage. I wanted to ask you if you think would be possible to...