Running commands with Snakemake
- “Before running Snakemake you need to write a Snakefile”
- “A Snakefile is a text file which defines a list of rules”
- “Rules have inputs, outputs, and shell commands to be run”
- “You tell Snakemake what file to make and it will run the shell command defined in the appropriate rule”
Running Snakemake on the cluster
- “Snakemake generates and submits its own batch scripts for your scheduler.”
- “You can store default configuration settings in a Snakemake profile”
- “
localrulesdefines rules that are executed locally, and never submitted to a cluster.”
Placeholders
- “Snakemake rules are made more generic with placeholders”
- “Placeholders in the shell part of the rule are replaced with values based on the chosen wildcards”
MPI applications and Snakemake
- “Snakemake chooses the appropriate rule by replacing wildcards such that the output matches the target”
- “Snakemake checks for various error conditions and will stop if it sees a problem”
Chaining rules
- “Snakemake links rules by iteratively looking for rules that make missing inputs”
- “Rules may have multiple named inputs and/or outputs”
- “If a shell command does not yield an expected output then Snakemake will regard that as a failure”
Processing lists of inputs
- “Use the
expand()function to generate lists of filenames you want to combine” - “Any
{input}to a rule can be a variable-length list”