declare the behavier: Reruns will not be triggered if the output file do not exist.

Hocnonsense · Hocnonsense · commit 4de03da2b2a6 · 2025-03-14T04:44:04.000+08:00
diff --git a/docs/snakefiles/rules.rst b/docs/snakefiles/rules.rst
@@ -70,7 +70,7 @@ It is not clear whether ``dataset=101.B`` and ``group=normal`` or ``dataset=101`
 Hence wildcards can be constrained to given regular expressions.
 Here we could restrict the wildcard ``dataset`` to consist of digits only using ``\d+`` as the corresponding regular expression.
 With Snakemake 3.8.0, there are three ways to constrain wildcards.
-First, a wildcard can be constrained within the file pattern, by appending a regular expression separated by a comma 
+First, a wildcard can be constrained within the file pattern, by appending a regular expression separated by a comma
 (you might want to use the `r` prefix for a raw string to avoid having to escape backslashes, particularly for more complex regular expressions):
 
 .. code-block:: python
@@ -214,7 +214,7 @@ These restrictions do not apply when using ``unpack()``.
 Helpers for defining rules
 --------------------------
 
-Snakemake provides a number of helpers that can be used to define rules and drastically simplify over using 
+Snakemake provides a number of helpers that can be used to define rules and drastically simplify over using
 :ref:`input functions <snakefiles-input_functions>` or :ref:`plain python expressions <snakefiles_aggregation>`.
 Below, we will first start with describing two basic helper functions for specifying aggregations and multiple output files.
 Afterwards, we will further show a set of semantic helper functions should increase readability and simplify code (see :ref:`snakefiles-semantic-helpers`).
@@ -346,14 +346,14 @@ The lookup function
 
 The ``lookup`` function can be used to look up a value in a python mapping (e.g. a ``dict``) or a `pandas dataframe or series <https://pandas.pydata.org>`_.
 It is especially useful for looking up information based on wildcard values.
-The ``lookup`` function has the signature 
+The ``lookup`` function has the signature
 
 .. code-block:: python
 
     lookup(
-        dpath: Optional[str | Callable] = None, 
-        query: Optional[str | Callable] = None, 
-        cols: Optional[List[str]] = None, 
+        dpath: Optional[str | Callable] = None,
+        query: Optional[str | Callable] = None,
+        cols: Optional[List[str]] = None,
         is_nrows: Optional[int],
         within=None,
         default=NODEFAULT
@@ -2668,8 +2668,9 @@ Assuming that the checkpoint is named ``somestep`` as above, the output files fo
 
 .. note::
 
-    Note that output files of checkpoints that are accessed via this mechanism should not be marked as temporary.
-    Otherwise, they would require to trigger reruns of the checkpoint whenever the DAG shall be reevaluated (because they are already missing at that point).
+    Note that output files of checkpoints that are accessed via this mechanism will not be marked as temporary.
+    Even you try to mark them as temporary, Snakemake will ignore the label and keep the output files of the checkpoint.
+    Reruns will not be triggered if the output file do not exist.
 
 Thereby, the ``get`` method throws ``snakemake.exceptions.IncompleteCheckpointException`` if the checkpoint has not yet been executed for these particular wildcard value(s).
 Inside an input function, the exception will be automatically handled by Snakemake, and leads to a re-evaluation after the checkpoint has been successfully passed.
@@ -3195,7 +3196,7 @@ The name is optional and can be left out, creating an anonymous rule. It can als
 
     for tool in ["bcftools", "freebayes"]:
         rule:
-            name: 
+            name:
                 f"call_variants_{tool}"
             input:
                 f"path/to/{tool}/inputfile"
