Coffea4bees workflows

List of workflows

This is a list of the workflows using Snakemake that we are using:

• Snakefile_reana: The workflow we use to launch the reana jobs.
• Snakefile_binoptimization: workflow to test the bin optimization of the SvB variable.

Useful commands

Snakemake workflows can be launch using the run_snakemake script, which internally using a snakemake container, then you can use it as:

cd python/
./run_snakemake --snakefile workflows/Snakefile_binoptimization 

Useful snakemake arguments: * --dry-run checks if all the rules are created correctly. Try to always run it as a test. * --printshellcmds along dry-run, it prints all the commands that the snakefile will execute * --rerun-incomplete to run partially workflows * --force in case some outputs are present, it will replace them by running the rules. * --cores X specifies the number of cores used. * --use-singularity if the rules uses a container