greedy by default (#1002)

* Update cli.py

* Update configuration_logging.smk

* Update configuration_logging.smk

* Update CHANGELOG.md

CHANGELOG.md

@@ -9,6 +9,10 @@ All changed fall under either one of these types: `Added`, `Changed`, `Deprecate
 
 ## [Unreleased]
 
+### Changed
+
+- use the snakemake greedy scheduler as default as the ilp scheduler struggles with "many" samples
+
 ## [1.0.3] - 2023-07-26
 
 ### Fixed

seq2science/cli.py

@@ -345,6 +345,7 @@ def _run(args, base_dir, workflows_dir, config_path):
     # get the additional snakemake options
     snakemake_options = args.snakemakeOptions if args.snakemakeOptions is not None else dict()
     snakemake_options.setdefault("config", {}).update({"rule_dir": os.path.join(base_dir, "rules")})
+    snakemake_options = snakemake_options | {"scheduler": "greedy"}
     snakemake_options["configfiles"] = [config_path]
     for key, value in snakemake_options.items():
         if not isinstance(value, str):

seq2science/rules/configuration_logging.smk

@@ -172,3 +172,4 @@ if not config.get("no_config_log"):
 
     logger.info(tabulate(table, headers=["config variable", "value"], tablefmt="pipe"))
     logger.info("\n\n")
+    logger.info(f"Using the snakemake {workflow.scheduler_type} scheduler.\n")