Describe the bug
I have overlooked that bug during the PR; now, while I was inspecting the logs more carefully I see that the rule which plots the sequence logos runs always for all N motifs but is also called N times (and it keeps overwritting results). What we would like to have is executing the rule N times, each of these calls should process 1 motif. Therefore the flag --input_files should be --input_file and it should just take one PWM file.
This is still a problem with incorrect expansions (expand). You should expand in the heatmap plotting rule not sequence logos plotting. Expansion is called after the rule which is being parallelized.
To Reproduce
Just clone the repository and run the integration test. Look closely at the snakemake logs @ the terminal.
Desktop (please complete the following information):
macOS Catalina
Travis CI builds
This is a pipeline processing bug - this issue should gain your priority
Describe the bug I have overlooked that bug during the PR; now, while I was inspecting the logs more carefully I see that the rule which plots the sequence logos runs always for all
Nmotifs but is also calledNtimes (and it keeps overwritting results). What we would like to have is executing the ruleNtimes, each of these calls should process1motif. Therefore the flag--input_filesshould be--input_fileand it should just take one PWM file. This is still a problem with incorrect expansions (expand). You should expand in the heatmap plotting rule not sequence logos plotting. Expansion is called after the rule which is being parallelized.To Reproduce Just clone the repository and run the integration test. Look closely at the snakemake logs @ the terminal.
Desktop (please complete the following information):
This is a pipeline processing bug - this issue should gain your priority