Unexpected keyword retries in rule definition (odp, line 294)

[LittleFrogHill]

Hi conchoecia,

Thank you for developing this nice pipeline.

I have a problem after I installed the software and run the test example.

snakemake --cores 10 -p --snakefile ../../scripts/odp
SyntaxError in line 294 of /home/shangao/software/odp/scripts/odp:
Unexpected keyword retries in rule definition (odp, line 294)

and I checked the line 294, it's look like:
286 params:
287 duplicate_handling = config["duplicate_proteins"]
288 benchmark: "benchmarks/check_input_legality/{sample}.check_input_legality.benchmark.txt"
289 resources:
290 io_slots = 1,
291 mem_mb = legality_get_mem_mb, # 20240105 - Got this from here: https://snakemake.readthedocs.io/en/stable/snakefile s/rules.html#dynamic-resources
292 runtime = 60 # 10 minutes
293 threads: 1
294 retries: 6
295 run:
296 # We always check to see if the chrom file is legal, regardless of whether we're ignoring duplicate prots.
297 if not odpf.chrom_file_is_legal(input.chrom):
298 raise IOError("The chrom file is not legal: {}".format(input.chrom))
299 if params.duplicate_handling not in ["fail", "pass"]:
300 raise IOError("duplicate_proteins in the config.yaml must be set to either 'fail' or 'pass'")
301 dup_proteins_allowed = False
302 if params.duplicate_handling == "pass":
303 dup_proteins_allowed = True
304

Do you know the reason, I used mamba installed the python libs and python version is 3.6.13

Bests,
Shan

[piamer]

Just adding on to say I am also getting this error! Did you find a fix?

[LittleFrogHill]

Just adding on to say I am also getting this error! Did you find a fix?

Sorry no, not yet