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Commit 8ff49ea0 authored by BIOPZ-Bak Maciej's avatar BIOPZ-Bak Maciej
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hardcode cluster log relative path into the slurm profiles

parent f4134a30
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Pipeline #13005 passed
jobscript: "../slurm-jobscript.sh"
cluster: "../slurm-submit.py"
cluster-status: "../slurm-status.py"
config: "cluster_logs='logs/cluster'"
snakefile: "../../workflow/Snakefile"
cores: 256
jobs: 256
......
jobscript: "../slurm-jobscript.sh"
cluster: "../slurm-submit.py"
cluster-status: "../slurm-status.py"
config: "cluster_logs='logs/cluster'"
snakefile: "../../workflow/Snakefile"
cores: 256
jobs: 256
......
......@@ -17,6 +17,10 @@
"type": "string",
"description": "Path to log directory."
},
"cluster_logs": {
"type": "string",
"description": "Path to cluster log directory."
},
"kallisto_indexes": {
"type": "string",
"description": "Path to kallisto indexes directory."
......
......@@ -38,11 +38,12 @@ except KeyError:
logger.warning(f"No rule config specified: using default values for all tools.")
# Create dir for cluster logs, if applicable
if cluster_config:
os.makedirs(
os.path.join(
os.getcwd(),
os.path.dirname(cluster_config['__default__']['out']),
onstart:
if config["cluster_logs"]:
os.makedirs(
os.path.join(
os.getcwd(),
config["cluster_logs"],
),
exist_ok=True)
......
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