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bentsherman avatar bentsherman commented on June 3, 2024 1

@pditommaso what if we allow clusterOptions to be a list of strings, then it becomes clear how to map the options to the directive lines:

clusterOptions = { [
  "-g /${_queue_group}",
  "-app ${params.fast_track ? params.lsf_fast_track_profile : task.process.tokenize(':')[-1].toLowerCase()}",
  "-sp ${params.hpc_priority}",
  "-P ${params.lsf_project_name}",
  "-rn" ] }

from nextflow.

bentsherman avatar bentsherman commented on June 3, 2024

It is because the abstract grid executor assumes the cluster options are provided as key-value pairs:

nextflow/modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy

Lines 95 to 116 in 7c9d965

String getHeaders( TaskRun task ) {
final token = getHeaderToken()
def result = new StringBuilder()
def header = new ArrayList(2)
def dir = getDirectives(task)
def len = dir.size()-1
for( int i=0; i<len; i+=2) {
def opt = dir[i]
def val = dir[i+1]
if( opt ) header.add(opt)
if( val ) header.add(wrapHeader(val))
if( header ) {
result << token << ' ' << header.join(' ') << '\n'
}
header.clear()
}
return result.toString()
}

So you can probably make clusterOptions work by inserting a blank value after -rn:

clusterOptions = { "-g /${_queue_group} -app ${params.fast_track ? params.lsf_fast_track_profile : task.process.tokenize(':')[-1].toLowerCase()} -sp ${params.hpc_priority} -P ${params.lsf_project_name} -rn ''" }

from nextflow.

pditommaso avatar pditommaso commented on June 3, 2024

It makes sense

from nextflow.

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