I am working on a snake-make workflow that follows the guidelines of formatting and linting so that it can be published on the official Snake-make repository. Whenever I push my code on GitHub, the GitHub actions are run and the pipeline is tested as indicated here.
The problem is related to the execution of some time-consuming rules, such as the genome indexing generation for bowtie. These rules are run every time and take plenty of time. I was wondering whether there was a way to bypass the execution of these rules and test the pipeline anyway. Do you have any suggestions about this?
A problem is that I have a rule in my snakemake workflow that downloads the human genome and that is needed to index and then for the alignment. I need a workaround to avoid this behaviour, since has you said it is not feasible to test on the whole genome.