step2_run_pipeline.sh

#!/bin/bash

# activate environment
#conda info --envs

# Usage: run_PRSCS.sh <GENOTYPES> <GWAS> <GWAS_N> <OUTDIR> <PHENO> <REF> <pirol|raven>
CLUSTER=${1}
GENOTYPES=${2}
GWAS=${3}
GWAS_N=${4}
OUTDIR=${5}
PHENO=${6}
REF=${7}
CONDA=${8}

shift

#echo "$@"

if [[ "$CLUSTER" == "pirol" ]]; then
    bash 02_run/01_run_PRSCS_on_pirol.sh "$@"
elif [[ "$CLUSTER" == "raven" ]]; then
    bash 02_run/01_run_PRSCS_on_raven.sh "$@"
else
    echo "❌ Unknown cluster: $CLUSTER"
    echo "Usage: run_PRSCS.sh <pirol|raven> GENOTYPES GWAS GWAS_N OUTDIR PHENO REF CONDA"
    exit 1
fi