Split pipelines

[jsgounot]

Hi,

Is there a way to run each snakemake pipeline individually? I understand the appeal of making one big executable that can run everything, but a more granulated approach would allow users to directly interface with snakemake arguments, which can be important in some cluster contexts. An example, using conda-prefix to avoid installing environments into the base directory.

Regards,
JS

[Russel88]

Hi JS

You can always run the snakefiles in MAGinator/maginator/workflow/*.Snakefile individually using the -s argument in snakemake, but then you need to add all the required inputs with --config, which can be cumbersome.

I think the best solution is that we add an argument for maginator which adds arguments to the snakemake command. Then, if you want to run each snakemake pipeline individually, you can use the --snake argument in maginator.

[jsgounot]

Hi Russel, sounds good!