accessing mem_mb from resources in params #3271
Description
Maybe this is not a bug but a wanted change in behavior in v8.
Snakemake version
- 8.27.1
Describe the bug
I started to move my pipelines from v7 to v8. In one of my rules I am accessing mem_mb from resources in params to calculate Gb -> Mb (stored in params.mem_gb). This worked so far without problems but now I am running into an error. I will first post my rule and then the error (log).
Any idea how to solve this? Thanks!
Rule
rule make_ref_dict:
message: "Create a GATK ref dictionary."
input:
reference = rules.reference.output.reference
output:
dict = REFERENCE_PREFIX + '.dict'
resources:
mem_mb = lambda wildcards, attempt: attempt * 2000,
cpus_per_task = 1
params:
mem_gb = lambda wildcards, resources: int(resources.mem_mb / 1000)
shell:
"""
picard -Xmx{params.mem_gb}g CreateSequenceDictionary -R {input.reference} -O {output.dict}
"""Logs
Building DAG of jobs...
InputFunctionException in rule variant-qc.make_ref_dict in file snakefile.smk, line 109:
Error:
TypeError: __int__ returned non-int (type TBDString)
Wildcards:
Traceback:
File "snakefile.smk", line 124, in <lambda> (rule variant-qc.make_ref_dict, line 153, snakefile.smk)