next.pbs

#!/bin/bash
#
# next.pbs
# 
# mads
# 2024-07-02
#
# This is a simple wrapper that that runs the DoBSeq workflow on NGC.
# The pipeline profile uses environment modules and runs all processes as submitted jobs.
#
#
# Usage:
#
#    myqsub [-F "optional arguments to Nexflow"] next.pbs
#

#PBS -l nodes=1:ppn=40:thinnode
#PBS -l walltime=24:00:00
#PBS -l mem=160gb
#PBS -j oe
#PBS -N nextflow

## exit if any errors or unset variables are encountered
set -euo pipefail

## Add environment variables for making Nextflow able to run wo. internet access.
name=nf_tools
version=2.0
root=/ngc/tools/ngctools/${name}/${version}
data=/ngc/shared/${name}

export NXF_SINGULARITY_CACHEDIR=${data}/containers
export NXF_ASSETS=${root}/pipelines
export NXF_SCM_FILE=${root}/scm
export NXF_PLUGINS_DIR=${data}/plugins

# Disable interactive logging
#export NXF_ANSI_LOG=false

module load tools ngctools jdk/21.0.1 nextflow/24.08.0-edge

nextflow_essential_params='-profile ngc -resume'

nextflow_command="nextflow run main.nf $nextflow_essential_params $@"

echo "-------- Log generated by nextflow.pbs -------" | tee -a nextflow.log
echo "Command: $0 $@" | tee -a nextflow.log
echo "User:" `whoami` | tee -a nextflow.log
echo "Date:" `date -Is` | tee -a nextflow.log
echo "PBS job ID: ${PBS_JOBID-none}" | tee -a nextflow.log
echo 'DoBSeq version:' `cat VERSION` | tee -a nextflow.log
echo 'git commit:' `(git rev-parse HEAD)` | tee -a nextflow.log
echo 'git status:' | tee -a nextflow.log
(git status -bs) | sed "s/^/    /" | tee -a nextflow.log
echo 'Nextflow version:' `nextflow -version` 2>&1 | tee -a nextflow.log
echo "Nextflow command: ${nextflow_command}" | tee -a nextflow.log

echo `date -Is` "--------------------- Starting Nextflow ---------------------" | tee -a nextflow.log

set +eo pipefail

${nextflow_command} 2>&1 | tee -a nextflow.log

echo `date -Is` "--------------------- Nextflow finished ---------------------" | tee -a nextflow.log

if [ -z ${PBS_JOBID+x} ]; then
    echo "This was not run as a PBS job" | tee -a nextflow.log
else
    echo "This was run as PBS job ${PBS_JOBID}" | tee -a nextflow.log
fi