From 1038cadd3839292e4732a95a615919f9344d6b41 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20K=C3=B6ster?= <johannes.koester@tu-dortmund.de>
Date: Wed, 16 Mar 2022 13:26:51 +0100
Subject: [PATCH] fix issue #1475

---
 snakemake/executors/__init__.py | 71 +++++++++++++++++----------------
 1 file changed, 37 insertions(+), 34 deletions(-)

diff --git a/snakemake/executors/__init__.py b/snakemake/executors/__init__.py
index ea0ca2db0..e617d240e 100644
--- a/snakemake/executors/__init__.py
+++ b/snakemake/executors/__init__.py
@@ -345,7 +345,11 @@ def format_job_pattern(self, pattern, job=None, **kwargs):
         if not job.is_branched and not job.is_updated:
             # Restrict considered rules. This does not work for updated jobs
             # because they need to be updated in the spawned process as well.
-            format_cli_arg("--allowed-rules", job.rules, quote=False)
+            rules = format_cli_arg("--allowed-rules", job.rules, quote=False)
+
+        job_specific_args = format_cli_arg(
+            "--local-groupid", job.jobid, skip=not job.is_group()
+        )
 
         target = format_cli_pos_arg(kwargs.get("target", job.get_targets()))
         snakefile = format_cli_pos_arg(kwargs.get("snakefile", self.snakefile))
@@ -357,6 +361,34 @@ def format_job_pattern(self, pattern, job=None, **kwargs):
         if "cores" in kwargs:
             del kwargs["cores"]
 
+        # wait for files and scheduler
+        scheduler_solver_path = ""
+        waitfiles_parameter = ""
+        if self.assume_shared_fs:
+            wait_for_files = []
+            wait_for_files.append(self.tmpdir)
+            wait_for_files.extend(job.get_wait_for_files())
+            # Prepend PATH of current python executable to PATH.
+            # This way, we ensure that the snakemake process in the cluster node runs
+            # in the same environment as the current process.
+            # This is necessary in order to find the pulp solver backends (e.g. coincbc).
+            scheduler_solver_path = format_cli_arg(
+                "--scheduler-solver-path", os.path.dirname(sys.executable)
+            )
+
+            # Only create extra file if we have more than 20 input files.
+            # This should not require the file creation in most cases.
+            if len(wait_for_files) > 20:
+                wait_for_files_file = self.get_jobscript(job) + ".waitforfilesfile.txt"
+                with open(wait_for_files_file, "w") as fd:
+                    print(wait_for_files, sep="\n", file=fd)
+
+                waitfiles_parameter = format_cli_arg(
+                    "--wait-for-files-file", wait_for_files_file
+                )
+            else:
+                waitfiles_parameter = format_cli_arg("--wait-for-files", wait_for_files)
+
         cmd = format(
             pattern,
             job=job,
@@ -370,6 +402,9 @@ def format_job_pattern(self, pattern, job=None, **kwargs):
             benchmark_repeats=job.benchmark_repeats if not job.is_group() else None,
             target=target,
             rules=rules,
+            job_specific_args=job_specific_args,
+            scheduler_solver_path=scheduler_solver_path,
+            waitfiles_parameter=waitfiles_parameter,
             **kwargs,
         )
         return cmd
@@ -769,50 +804,18 @@ def get_jobscript(self, job):
         return os.path.join(self.tmpdir, f)
 
     def format_job(self, pattern, job, **kwargs):
-        wait_for_files = []
-        scheduler_solver_path = ""
-        if self.assume_shared_fs:
-            wait_for_files.append(self.tmpdir)
-            wait_for_files.extend(job.get_wait_for_files())
-            # Prepend PATH of current python executable to PATH.
-            # This way, we ensure that the snakemake process in the cluster node runs
-            # in the same environment as the current process.
-            # This is necessary in order to find the pulp solver backends (e.g. coincbc).
-            scheduler_solver_path = format_cli_arg(
-                "--scheduler-solver-path", os.path.dirname(sys.executable)
-            )
-
-        # Only create extra file if we have more than 20 input files.
-        # This should not require the file creation in most cases.
-        if len(wait_for_files) > 20:
-            wait_for_files_file = self.get_jobscript(job) + ".waitforfilesfile.txt"
-            with open(wait_for_files_file, "w") as fd:
-                print(wait_for_files, sep="\n", file=fd)
-
-            waitfiles_parameter = format_cli_arg(
-                "--wait-for-files-file", wait_for_files_file
-            )
-        else:
-            waitfiles_parameter = format_cli_arg("--wait-for-files", wait_for_files)
-        job_specific_args = format_cli_arg(
-            "--local-groupid", job.jobid, skip=not job.is_group()
-        )
-
         format_p = partial(
             self.format_job_pattern,
             job=job,
             properties=job.properties(cluster=self.cluster_params(job)),
             latency_wait=self.latency_wait,
-            waitfiles_parameter=waitfiles_parameter,
-            scheduler_solver_path=scheduler_solver_path,
-            job_specific_args=job_specific_args,
             **kwargs,
         )
         try:
             return format_p(pattern)
         except KeyError as e:
             raise WorkflowError(
-                "Error formatting jobscript: {} not found\n"
+                "Error formatting job: {} not found\n"
                 "Make sure that your custom jobscript is up to date.".format(e)
             )