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Snakemake logger improvements #157

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Merged
henricasanova merged 5 commits into from
May 13, 2026
Merged

Snakemake logger improvements #157

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dcd2e4a
Making snakemake logger more robust
henricasanova May 12, 2026
1fb1d20
Snakemake logger enhancements: capture #threads for each task
henricasanova May 12, 2026
43689bc
Skipping Snakemake benchmark files when parsing Snakemake logs
henricasanova May 13, 2026
41613bd
Ignoring "(cached)" files when parsing Snakemake logs
henricasanova May 13, 2026
faedb6b
Ignoring LOG files when parsing Snakemake logs
henricasanova May 13, 2026
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11 changes: 11 additions & 0 deletions wfcommons/wfinstances/logs/snakemake.py
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Original file line number Diff line number Diff line change
Expand Up @@ -73,6 +73,7 @@ def __init__(self,
self.file_objects = {}
self.task_map = {}
self.task_shell = {}
self.task_threads = {}
self.task_input_files = {}
self.task_output_files = {}
self.file_input_output = {}
Expand Down Expand Up @@ -140,6 +141,7 @@ def _build_task_map(self):
for row in rows:
task_idx = row[0]
rule_idx = row[3]
threads = int(row[9])
# Shell command
if row[8]:
command_list = [x.rstrip().lstrip() for x in row[8].lstrip().rstrip().split('\n')]
Expand All @@ -150,6 +152,7 @@ def _build_task_map(self):
continue
self.task_map[task_idx] = rules[rule_idx] + "_" + str(task_idx)
self.task_shell[task_idx] = shell_cmd
self.task_threads[task_idx] = threads
self.task_input_files[task_idx] = []
self.task_output_files[task_idx] = []

Expand All @@ -159,10 +162,17 @@ def _build_file_map(self):
cursor.execute("SELECT * FROM files")
rows = cursor.fetchall()
for row in rows:
file_type = row[2]
# Skip snakemake's BENCHMARK files (and besides snkmt doesn't deal with them correctly!)
# and LOG files (which sometimes are missing anyway)
if file_type == "BENCHMARK" or file_type == "LOG":
continue
task_idx = row[3]
if task_idx not in self.task_input_files and task_idx not in self.task_output_files:
continue
full_path = row[1]
# clean path
full_path = full_path.split(" (access:")[0].split(" (cached)")[0].strip()
if self.path_prefix_rewrite:
full_path = full_path.replace(self.path_prefix_rewrite[0], self.path_prefix_rewrite[1])
file_size = os.path.getsize(f"{full_path}")
Expand Down Expand Up @@ -216,6 +226,7 @@ def _create_tasks(self):
input_files=input_files,
output_files=output_files,
program=program_name,
cores=self.task_threads[idx],
args=program_args,
logger=self.logger)
self.workflow.add_task(task)
Expand Down
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