Minor update to the Snakemake documentation and test code

Author: henricasanova

tests/translators_loggers/test_translators_loggers.py

@@ -223,7 +223,7 @@ def run_workflow_makeflow(container, num_tasks, str_dirpath):
 
 def run_workflow_snakemake(container, num_tasks, str_dirpath):
     # Run the workflow (with full logging)
-    exit_code, output = container.exec_run(cmd=["bash", "-c", "snakemake -s ./workflow.smk --cores 1 --logger snkmt --logger-snkmt-db ./snkmt.sqlite"],
+    exit_code, output = container.exec_run(cmd=["bash", "-c", "snakemake -s ./workflow.smk --cores 1 --logger snkmt --logger-snkmt-db --no-temp ./snkmt.sqlite"],
                                            user="wfcommons", stdout=True, stderr=True)
     # Check sanity
     assert (exit_code == 0)

wfcommons/wfinstances/logs/snakemake.py

@@ -29,8 +29,9 @@
 class SnakemakeLogsParser(LogsParser):
     """
     Parse a Snakemake execution directory to generate workflow instance. It requires the path of
-    a sqlite database file generated by the `snkmt` logger plugin when the workflow is executed
-    as `snakemake ----logger snkmt --logger-snkmt-db ./snkmt.sqlite ...`
+    a sqlite database file generated by the `snkmt` logger plugin. It also requires that all temp
+    files be preserved. In other words the workflow should be executed as
+    as `snakemake --logger snkmt --logger-snkmt-db ./snkmt.sqlite --no-temp ...`
 
     :param execution_dir: Snakemake execution dir (all workflow input/output file, and also typically the Snakefile).
     :type execution_dir: pathlib.Path
@@ -187,4 +188,4 @@ def _create_tasks(self):
             for input_idx in input_to:
                 for output_idx in output_from:
                     # print(f"Adding dependency: {self.task_map[output_idx]} --> {self.task_map[input_idx]}")
-                    self.workflow.add_dependency(self.task_map[output_idx], self.task_map[input_idx])
+                    self.workflow.add_dependency(self.task_map[output_idx], self.task_map[input_idx])