execute.script

#!/usr/bin/env bash

export NXF_HOME="/hps/nobackup/cochrane/ena/users/sands/1k"
######################################################################################
##
## FIRST SECTION:
## Here we define the requirements we need to run our job: CPUs, RAM, run time, ...
##
######################################################################################

#BSUB -J nanopore_1ktest_job # job name
#BSUB -W 00:10      # wall-clock time (hrs:mins)
#BSUB -n 1          # number of tasksi/CPUs in job
#BSUB -q standard   # queue
#BSUB -e error.%J   # error file name in which %J is replaced by the job ID
#BSUB -o output.%J  # output file name in which %J is replaced by the job ID




######################################################################################
##
## SECOND SECTION:
## Here we define the modules we need to be loaded in order to run our job.
## In this case, we need to load the R module, ... but first we make sure
## we start off with a sane, blank environment so we purge all modules
##
######################################################################################

module purge

module load nextflow-20.07.1-gcc-9.3.0-mqfchke

nextflow -C /homes/sands/nanopore/nextflow.config run /homes/sands/code/ENA_SARS_Cov2_nanopore/nanopore1k.nf -with-singularity /homes/sands/nanopore/ena-sars-cov2-nanopore.sif >> /hps/nobackup/cochrane/ena/users/sands/1k/1koutput -profile lsf -w /hps/nobackup/cochrane/ena/users/sands/1k/workdir