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fix: create jobname with wildcards of all jobs in job groups #8

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merged 2 commits into from
Jun 3, 2024
Merged

fix: create jobname with wildcards of all jobs in job groups #8

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cb0eade
fix: create jobname with wildcards of all jobs in job groups
dlaehnemann May 28, 2024
1b2bc0c
fix line lengths for linter
dlaehnemann May 28, 2024
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16 changes: 14 additions & 2 deletions snakemake_executor_plugin_lsf/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,9 +76,21 @@ def run_job(self, job: JobExecutorInterface):
# with job_info being of type
# snakemake_interface_executor_plugins.executors.base.SubmittedJobInfo.

log_folder = f"group_{job.name}" if job.is_group() else f"rule_{job.name}"
if job.is_group():
# use the group name, which is in groupid
log_folder = f"group_{job.groupid}"
# get all wildcards of all the jobs in the group and
# prepend each with job name, as wildcards of same
# name can contain different values across jobs
wildcard_dict = {
f"{j.name}__{k}": v
for j in job.jobs
for k, v in j.wildcards_dict.items()
}
else:
log_folder = f"rule_{job.name}"
wildcard_dict = job.wildcards_dict

wildcard_dict = job.wildcards_dict
if wildcard_dict:
wildcard_dict_noslash = {
k: v.replace("/", "___") for k, v in wildcard_dict.items()
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