Snakemake parameter
Bohra passed args.cpus to SnpDetection object self.cpus during the initial
Then, there is a func name: set_snakemake_jobs() to double check whether the self.cpus is over the limitation:
SnpDetection.py#L141
def set_snakemake_jobs(self):
'''
set the number of jobs to run in parallel based on the number of cpus from args
'''
if int(self.cpus) < int(psutil.cpu_count()):
self.jobs = self.cpus
else:
self.jobs = 1
However, in the final command line to run snakemake file, it does not use self.jobs.
if self.cluster:
cmd = f"{self.cluster_cmd()} -s {snake_name} -d {wd} {force} {singularity_string} --latency-wait 1200"
else:
cmd = f"snakemake {dry} -s {snake_name} {singularity_string} -j {self.cpus} -d {self.job_id} {force} --verbose 2>&1"
kristyhoran
commented
2 years ago
Snakemake parameter Bohra passed args.cpus to SnpDetection object self.cpus during the initial Then, there is a func name: set_snakemake_jobs() to double check whether the self.cpus is over the limitation: SnpDetection.py#L141 def set_snakemake_jobs(self): ''' set the number of jobs to run in parallel based on the number of cpus from args ''' if int(self.cpus) < int(psutil.cpu_count()): self.jobs = self.cpus else: self.jobs = 1 However, in the final command line to run snakemake file, it does not use self.jobs. if self.cluster: cmd = f"{self.cluster_cmd()} -s {snake_name} -d {wd} {force} {singularity_string} --latency-wait 1200" else: cmd = f"snakemake {dry} -s {snake_name} {singularity_string} -j {self.cpus} -d {self.job_id} {force} --verbose 2>&1"