Fix _test_script

Author: Ulthran

sunbeam/scripts/run.py

@@ -18,13 +18,12 @@ def main(argv: list[str] = sys.argv):
 
     sc = SunbeamConfig.from_file(configfile)
     Cfg = sc.resolved_paths()
-    log_fp = Cfg["all"]["log_fp"]
 
     # From here on everything is considered part of the "pipeline"
     # This means all logs are handled by the pipeline logger (or pipeline extension loggers)
     # You could argue it would make more sense to start this at the actual snakemake call
     # but this way we can log some relevant setup information that might be useful on post-mortem analysis
-    logger = get_pipeline_logger(log_fp)
+    logger = get_pipeline_logger()
 
     snakefile = Path(__file__).parent.parent / "workflow" / "Snakefile"
     if not snakefile.exists():

sunbeam/workflow/Snakefile

@@ -20,7 +20,7 @@ MIN_RUNTIME = int(os.getenv("SUNBEAM_MIN_RUNTIME", 15))
 
 sc = SunbeamConfig(config)
 Cfg = sc.resolved_paths()
-logger = get_pipeline_logger(Cfg["all"]["log_fp"])
+logger = get_pipeline_logger()
 logger.debug(f"Sunbeam configuration: {Cfg}")
 
 # Load extensions

sunbeam/workflow/scripts/_test_script.py

@@ -1,4 +1,9 @@
+from pathlib import Path
+
+
 l = snakemake.log[0]
+o = Path(snakemake.output[0])
+
 with open(l, "w") as log:
     log.write("HERE\n")
 
@@ -9,3 +14,5 @@
     logger.info("This works!")
 
     SampleList()
+
+    o.write_text("This is a test output file.\n")