When Snakemake is executed with -retries 3, it will try to restart a failed job 3 times before it gives up. This is handy when executing a Snakemake workflow in a cluster environment, where jobs can e.g. The parameter attempt allows us to adjust resources based on how often the job has been restarted (see All Options, option -retries). The signature of the callable must be callable(wildcards ) ( input, threads, and attempt are optional parameters). They can also be callables that return int or str values. Resources can have any arbitrary name, and must be assigned int or str values. If no limits are given, the resources are ignored in local execution. Similarly, deepcopy () return a deep copy of x. For example: import copy py (x) epcopy (x) Here, the copy () return a shallow copy of x. Suppose, you need to copy the compound list say x. to limit IO-heavy jobs by assigning an artificial IO-resource to them and limiting it via the -resources flag. We use the copy module of Python for shallow and deep copy operations. with a limited number of additional devices like GPUs) this allows us to control scheduling in various ways, e.g. Instead, resources are used to determine which jobs can be executed at the same time without exceeding the limits specified at the command line.Īpart from making Snakemake aware of hybrid-computing architectures (e.g. In general, resources are just names to the Snakemake scheduler, i.e., Snakemake does not check on the resource consumption of jobs in real time. above mem_mb=100 in rule a means that any job from rule a will require 100 megabytes of memory in total, and not per thread). Resources are always meant to be specified as total per job, not by thread (i.e. The scheduler will ensure that the given resources are not exceeded by running jobs. In addition to threads, a rule can use arbitrary user-defined resources by specifying them with the resources-keyword: It is also possible to refer to a predefined variable (e.g, threads: threads_max) so that the number of cores for a set of rules can be changed with one change only by altering the value of the variable threads_max. The signature of the callable should be callable(wildcards) (input is an optional parameter). Starting from version 3.7, threads can also be a callable that returns an int value. Snakemake will always round the calculated value down (while enforcing a minimum of 1 thread). E.g., in the above example, we reserve 75% of the given cores for the rule. The number of given cores is globally available in the Snakefile as an attribute of the workflow object: res.Īny arithmetic operation can be performed to derive a number of threads from this. Rule NAME : input : "path/to/inputfile", "path/to/other/inputfile" output : "path/to/outputfile", "path/to/another/outputfile" shell : "somecommand " Integrating foreign workflow management systems.Onstart, onsuccess and onerror handlers.Ensuring output file properties like non-emptyness or checksum compliance.
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