Nextflow

nextflow.config

executor.$pbspro.queueSize = 50

tutorial.nf

#!/usr/bin/env nextflow

params.str = 'Hello world!'

process splitLetters {

    executor = 'local'

    output:
    file 'chunk_*' into letters

    """
    printf '${params.str}' | split -b 6 - chunk_
    """
}


process convertToUpper {

    label = 'throughput'

    input:
    file x from letters.flatten()

    output:
    stdout result

    """
    cat $x | tr '[a-z]' '[A-Z]'
    """
}

result.view { it.trim() }

tutorial.nf.diff

 #!/usr/bin/env nextflow
 
 params.str = 'Hello world!'
 
 process splitLetters {
 
+    executor = 'local'
+
     output:
     file 'chunk_*' into letters
 
     """
     printf '${params.str}' | split -b 6 - chunk_
     """
 }
 
 
 process convertToUpper {
+
+    label = 'throughput'
 
     input:
     file x from letters.flatten()
 
     output:
     stdout result
 
     """
     cat $x | tr '[a-z]' '[A-Z]'
     """
 }
 
 result.view { it.trim() }
 

tutorial.pbs.sh

#!/usr/bin/env bash
#PBS -l walltime=00:30:00,select=1:ncpus=1:mem=1g
cd $PBS_O_WORKDIR
module load nextflow/20.01.0
nextflow run tutorial.nf