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Snakemake logger minor fixes #158

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Merged
henricasanova merged 2 commits into from
May 21, 2026
Merged

Snakemake logger minor fixes #158

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257db3b
Using shlex to split task's command-line into arguments
henricasanova May 21, 2026
df7a707
Bug fix (in case of unknown program/args for a task)
henricasanova May 21, 2026
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38 changes: 23 additions & 15 deletions wfcommons/wfinstances/logs/snakemake.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
import math
import os
import pathlib
import shlex

from datetime import datetime, timezone
from logging import Logger
Expand Down Expand Up @@ -213,22 +214,29 @@ def _create_tasks(self):

if self.task_shell[idx]:
program_name = self.task_shell[idx].split(' ')[0]
program_args = self.task_shell[idx].split(' ')[0:]
program_args = shlex.split(self.task_shell[idx], posix=False)
task = Task(name=self.task_map[idx],
task_id=self.task_map[idx],
task_type=TaskType.COMPUTE,
runtime=elapsed,
executed_at=start_date,
input_files=input_files,
output_files=output_files,
program=program_name,
cores=self.task_threads[idx],
args=program_args,
logger=self.logger)
else:
program_name = "n/a"
program_args = []

task = Task(name=self.task_map[idx],
task_id=self.task_map[idx],
task_type=TaskType.COMPUTE,
runtime=elapsed,
executed_at=start_date,
input_files=input_files,
output_files=output_files,
program=program_name,
cores=self.task_threads[idx],
args=program_args,
logger=self.logger)
task = Task(name=self.task_map[idx],
task_id=self.task_map[idx],
task_type=TaskType.COMPUTE,
runtime=elapsed,
executed_at=start_date,
input_files=input_files,
output_files=output_files,
cores=self.task_threads[idx],
logger=self.logger)

self.workflow.add_task(task)

# File dependencies
Expand Down
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