run_nextflow_sma_umcu.sh

#!/bin/bash
set -euo pipefail

workflow_path='/hpc/diaggen/projects/ONT_SMA_project/software/NextflowSMA'

# Set input and output dirs
echo " #### Running method targeted SMA specific + adaptive sequencing ####"
input_path=`realpath -e $1`
output=$2
email=$3
sample_id=$4
start_run=$5
ploidy=$6
optional_params=( "${@:7}" )

mkdir -p $output && cd $output
mkdir -p log

if ! { [ -f 'workflow.running' ] || [ -f 'workflow.done' ] || [ -f 'workflow.failed' ]; }; then
touch workflow.running

sbatch <<EOT
#!/bin/bash
#SBATCH --time=144:00:00
#SBATCH --nodes=1
#SBATCH --mem 10G
#SBATCH --gres=tmpspace:16G
#SBATCH --job-name HapSMA
#SBATCH -o log/slurm_nextflow_ont.%j.out
#SBATCH -e log/slurm_nextflow_ont.%j.err
#SBATCH --mail-user $email
#SBATCH --mail-type FAIL
#SBATCH --export=NONE

export NXF_JAVA_HOME='$workflow_path/tools/java/jdk'

$workflow_path/tools/nextflow/nextflow run $workflow_path/SMA.nf \
-c $workflow_path/SMA.config -c $workflow_path/SMA_umcu.config \
--input_path $input_path \
--outdir $output \
--email $email \
--sample_id $sample_id \
--start $start_run \
--ploidy $ploidy \
${optional_params[@]:-""} \
-profile slurm \
-resume -ansi-log false

if [ \$? -eq 0 ]; then
    echo "Nextflow done."

    #  echo "Zip work directory"
    find work -type f | egrep "\.(command|exitcode)" | zip -@ -q work.zip

    #  echo "Remove work directory"
    rm -r work

    #  echo "Creating md5sum"
    find -type f -not -iname 'md5sum.txt' -exec md5sum {} \; > md5sum.txt

    echo "SMA workflow completed successfully."
    rm workflow.running
    touch workflow.done

    exit 0
else
    echo "Nextflow failed"
    rm workflow.running
    touch workflow.failed
    exit 1
fi
EOT
else
echo "Workflow job not submitted, please check $output for 'workflow.status' files."
fi