The slurm executor scope got ignored inside of config profile - bug or feature?
Closed this issue · 1 comments
qiyubio commented
While composing the config file for HPC, I found that the slurm executor scope listed inside of profile got ignored (example 3) , so by default the pollInterval will be 5s, which is very unfriendly for multiple-users cluster, but the setting works in process scope outside of profile (example 2), is it a bug or feature?
e.g.1 worked example nextflow.conf:
executor {
pollInterval = '2 min'
}
profile1 {
...
}
run with
nextflow run -profile profile1 xxx
.nextflow.log
pollInterval: 2m
e.g. 2 worked example nextflow.conf:
process {
pollInterval = '2 min'
...
}
run with
nextflow run -c nextflow.conf xxx
.nextflow.log
pollInterval: 2m
e.g. 3 failed example nextflow.conf:
profile2 {
process {
pollInterval = '2 min'
...
}
}
run with
nextflow run -profile profile2 xxx
.nextflow.log
pollInterval: 5s
qiyubio commented
Since this only happens on non nf-core pipeline, I will send the issue to nextflow repo instead.