fix: keep flags with apply_wildcards on cloned IOFile

snakemake/dag.py

@@ -280,7 +280,7 @@ def create_conda_envs(
         env_set = {
             (job.conda_env_spec, job.container_img_url)
             for job in jobs
-            if job.conda_env_spec
+            if job.conda_env_spec and (self.workflow.run_local or job.is_local)
         }
         # Then based on md5sum values
         self.conda_envs = dict()

snakemake/executors/google_lifesciences.py

@@ -62,7 +62,7 @@ def __init__(
         # Attach variables for easy access
         self.workflow = workflow
         self.quiet = quiet
-        self.workdir = os.path.dirname(self.workflow.persistence.path)
+        self.workdir = os.path.realpath(os.path.dirname(self.workflow.persistence.path))
         self._save_storage_cache = cache
 
         # Relative path for running on instance
@@ -631,7 +631,7 @@ def _generate_build_source_package(self):
         """
         # Workflow sources for cloud executor must all be under same workdir root
         for filename in self.workflow_sources:
-            if self.workdir not in filename:
+            if self.workdir not in os.path.realpath(filename):
                 raise WorkflowError(
                     "All source files must be present in the working directory, "
                     "{workdir} to be uploaded to a build package that respects "

snakemake/io.py

@@ -735,7 +735,7 @@ def format_dynamic(self):
     def clone_flags(self, other):
         if isinstance(self._file, str):
             self._file = AnnotatedString(self._file)
-        if isinstance(other._file, AnnotatedString):
+        if isinstance(other._file, AnnotatedString) or isinstance(other._file, _IOFile):
             self._file.flags = getattr(other._file, "flags", {}).copy()
             if "remote_object" in self._file.flags:
                 self._file.flags["remote_object"] = copy.copy(

snakemake/rules.py

@@ -892,7 +892,6 @@ def concretize_param(p, wildcards, is_from_callable):
         def handle_incomplete_checkpoint(exception):
             """If checkpoint is incomplete, target it such that it is completed
             before this rule gets executed."""
-            print(exception.targetfile)
             if exception.targetfile in input:
                 return TBDString()
             else:

tests/test_cloud_checkpoints_issue574/Snakefile

@@ -19,9 +19,14 @@ checkpoint copy:
     run:
         shell("cp {input} {output}")
 
+def get_pack_input(wildcards):
+    output = checkpoints.copy.get().output[0]
+    return output
+
+
 rule pack:
     input:
-        lambda wildcards: checkpoints.copy.get().output[0]
+        get_pack_input
     output:
         "landsat-data.txt.bz2"
     conda: