Describe the solution you'd like
Extend the pipeline by one more step which will generate sequence logos for all the motifs (in PWM format) provided by the user.
Additional context
Let's take it step-by step. As I mentioned previously, calling a python script from within an R script from within snakemake pipeline is a bad practice. So let's add another rule with will call a script to generate png images with sequence logos for all motifs provided in a directory by the user.
Such rule could start directly after create_results_directory since it does not need to wait for any other input generated during the processing, right?
This rule would have to be executed in parallel for every motif the user provides. Take a look at the rule combine_MotEvo_results and recall the expand() mechanism which allows you for such tricks. You will need to add a list of images with expand() to the all rule as well (as an input, since the all rule gathers everything).
Describe the solution you'd like Extend the pipeline by one more step which will generate sequence logos for all the motifs (in PWM format) provided by the user.
Additional context Let's take it step-by step. As I mentioned previously, calling a
pythonscript from within anRscript from withinsnakemakepipeline is a bad practice. So let's add another rule with will call a script to generatepngimages with sequence logos for all motifs provided in a directory by the user.Such rule could start directly after
create_results_directorysince it does not need to wait for any other input generated during the processing, right? This rule would have to be executed in parallel for every motif the user provides. Take a look at the rulecombine_MotEvo_resultsand recall theexpand()mechanism which allows you for such tricks. You will need to add a list of images withexpand()to theallrule as well (as an input, since theallrule gathers everything).