fix: fixed bug in missing input file handling for cluster jobs (#1544)

snakemake · Mar 31, 2022 · 40e2eb2 · 40e2eb2
1 parent e820f97
commit 40e2eb2
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Showing 25 changed files with 6 additions and 3 deletions.
diff --git a/snakemake/executors/__init__.py b/snakemake/executors/__init__.py
@@ -767,7 +767,7 @@ def get_job_args(self, job):
             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)
+                    print(*wait_for_files, sep="\n", file=fd)
 
                 waitfiles_parameter = format_cli_arg(
                     "--wait-for-files-file", wait_for_files_file

diff --git a/snakemake/io.py b/snakemake/io.py
@@ -821,7 +821,8 @@ def get_missing():
             "Waiting at most {} seconds for missing files.".format(latency_wait)
         )
         for _ in range(latency_wait):
-            if not get_missing():
+            missing = get_missing()
+            if not missing:
                 return
             time.sleep(1)
         missing = "\n".join(get_missing())

diff --git a/tests/test14/Snakefile.nonstandard b/tests/test14/Snakefile.nonstandard
@@ -12,7 +12,9 @@ rule all:
 	input: 'test.predictions', 'test.2.inter2'
 
 rule compute1:
-	input: '{name}.in'
+	input:
+            '{name}.in',
+            expand("raw.{i}.txt", i=range(22))
 	output: ['{name}.%s.inter'%c for c in chromosomes]
         params: prefix="{name}"
 	run:

diff --git a/tests/test14/raw.0.txt b/tests/test14/raw.0.txt
diff --git a/tests/test14/raw.1.txt b/tests/test14/raw.1.txt
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diff --git a/tests/test14/raw.9.txt b/tests/test14/raw.9.txt