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fix: fixed bug in missing input file handling for cluster jobs (#1544)
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johanneskoester committed Mar 31, 2022
1 parent e820f97 commit 40e2eb2e6c6e31c7cc590c8d643e0640e9377aa4
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Showing 25 changed files with 6 additions and 3 deletions.
@@ -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
@@ -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())
@@ -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:
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