#!/bin/bash
#SBATCH --job-name=sarek_C90159
#SBATCH --output=logs/sarek_C90159_%j.log
#SBATCH --error=logs/sarek_C90159_%j.err
#SBATCH --time=72:00:00
#SBATCH --mem=32G
#SBATCH --cpus-per-task=8

source $(conda info --base)/etc/profile.d/conda.sh
conda activate nextflow

module load apptainer

export NXF_SINGULARITY_CACHEDIR=/shares/stucklin.mef.uzh/vkanch/CBTN_CAVATICA_WGS/nf-core_sarek/singularity_cache
export NXF_JVM_ARGS="-Xms512m -Xmx4g"

nextflow run nf-core/sarek \
    -r 3.8.1 \
    -offline \
    -c nextflow.config \
    --input samplesheet_C90159.csv \
    --outdir results_C90159/ \
    --genome GATK.GRCh38 \
    --step variant_calling \
    --tools mutect2 \
    -profile singularity