nf-core/configs

The slurm executor scope got ignored inside of config profile - bug or feature?

Closed this issue · 1 comments

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

Since this only happens on non nf-core pipeline, I will send the issue to nextflow repo instead.