I have a massive Snakefile. The bits that are likely important are these below. I want to make this a bit more flexible with input files. in the runini file; if lanenumlanelaeve = 1, I want snakemake ...

How can I use relative paths in my configuration file so that users do not need to change USER in the paths for output directories? I have this: config.yml proj_name: H1N1_rhesus contact: email: use...

I need to concatenate certain files inside some directories that have been created using a wildcard in a Snakefile. I tried to create the following rule to concatenate all files inside these directori...

I try to run all the rules by followed commands: touch scripts/*.py snakemake --cores <YOUR NUMBER> The problem is my local internet connection is unstable, I could submit the command through p...