diff --git a/launch.sh b/launch.sh index 0d171ea..d1a20e4 100644 --- a/launch.sh +++ b/launch.sh @@ -13,22 +13,16 @@ module load nextflow/23.04.1 run_dir_path=$1 fcid=$2 -entry=$3 +entry="${3:+-entry $3}" log_dir="/scratch/gencore/GENEFLOW/alpha/logs/${fcid}/pipeline" -nextflow_command="nextflow \ - -log ${log_dir}/nextflow.log run /home/gencore/SCRIPTS/GENEFLOW/main.nf \ +nextflow \ + -log ${log_dir}/nextflow.log \ + run gencorefacility/GENEFLOW \ -c /home/gencore/SCRIPTS/GENEFLOW/nextflow.config \ --run_dir_path $run_dir_path \ --trace_file_path ${log_dir}/trace.txt \ - -with-report ${log_dir}/${fcid}_report.html" - -# Check if the third parameter (entry point) is provided and append to the command -if [ ! -z "$entry" ]; then - nextflow_command="$nextflow_command -entry $entry" -fi - -# Execute the command -eval $nextflow_command + -with-report ${log_dir}/${fcid}_report.html \ + ${entry}