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Description
I have the following definition in my profile. Yet the parenthesis in the job names are not replaced.
executor {
name = 'slurm'
queueSize = 70
submitRateLimit = '10 sec'
jobName = {
n = "${task.name}" -> n.replaceAll('[():\\\s]', '_')
}
}
therefore I get these kind of errors:
Caused by:
Failed to submit process to grid scheduler for execution
Command executed:
sbatch .command.run
Command exit status:
1
Command output:
sbatch: error: Illegal character in job name at position 27. Valid characters are lowercase a to z, uppercase A to Z, numbers 0 to 9, period (.), underscore (_), forward slash (/) and hyphen (-).
sbatch: error: Batch job submission failed: Unspecified error
If I look at the .command.run file, the job name is set to:
#SBATCH -J nf-NFCORE_MAG_MAG_MEGAHIT_(sample1)
I tried the java regex on https://regex101.com/ where it replaces the parenthesis correctly.
Any help to get this working is appreciated
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