nextflow run nf-core/sarek \
        -r 3.8.1 \
        -profile apptainer \
        -c alma_config.txt \
        --input $samplesheet \
        --outdir ./results/${run_name}/ \
        --genome GATK.GRCh38 \
        --tools mutect2,ascat,vep \
        --download_cache TRUE \
        --wes TRUE \
	--pon /data/scratch/DRI/URTHY/TARGTHER/gseed/Pipelines/sarek/data/pon/haystack_batch1/haystack_batch1.pon.vcf.gz \
        --pon_tbi /data/scratch/DRI/URTHY/TARGTHER/gseed/Pipelines/sarek/data/pon/haystack_batch1/haystack_batch1.pon.vcf.gz.tbi \
	--nucleotides_per_second 200000 \
        --trim_fastq TRUE \
	--vep_include_fasta TRUE \
	--vep_custom_args "--hgvs --everything --pick --total_length --offline --format vcf" \
        --vep_dbnsfp TRUE \
	--dbnsfp /data/scratch/DRI/URTHY/TARGTHER/gseed/Pipelines/sarek/data/dbNSFP/4_9/dbNSFPv4.9a_custombuild.gz \
	--dbnsfp_tbi /data/scratch/DRI/URTHY/TARGTHER/gseed/Pipelines/sarek/data/dbNSFP/4_9/dbNSFPv4.9a_custombuild.gz.tbi \
	--dbnsfp_fields "Ensembl_transcriptid,CADD_phred_hg19,CADD_raw_hg19,FATHMM_pred,FATHMM_score,GERP++_RS,LRT_pred,LRT_score,MutationAssessor_pred,MutationAssessor_score,MutationTaster_pred,MutationTaster_score,REVEL_score,VEST4_score,MetaSVM_pred,M-CAP_pred,BayesDel_noAF_pred,ClinPred_pred,clinvar_clnsig,clinvar_id,AlphaMissense_pred,AlphaMissense_score" \
	--intervals /data/scratch/DRI/URTHY/TARGTHER/gseed/Pipelines/sarek/data/battenberg_ascat_loci_sarek/final_wes_ref_files_hg38/chr/final_padded_hg38_wes_targets_chr_sorted.bed \
        --joint_mutect2 TRUE \
        --ascat_alleles /data/scratch/DRI/URTHY/TARGTHER/gseed/Pipelines/sarek/data/battenberg_ascat_loci_sarek/ascatrepo/G1000_alleles_hg38.zip \
        --ascat_loci /data/scratch/DRI/URTHY/TARGTHER/gseed/Pipelines/sarek/data/battenberg_ascat_loci_sarek/ascatrepo/G1000_loci_hg38.zip \
        --ascat_loci_gc /data/scratch/DRI/URTHY/TARGTHER/gseed/Pipelines/sarek/data/battenberg_ascat_loci_sarek/ascatrepo/GC_G1000_hg38.zip \
        --ascat_loci_rt /data/scratch/DRI/URTHY/TARGTHER/gseed/Pipelines/sarek/data/battenberg_ascat_loci_sarek/ascatrepo/RT_G1000_hg38.zip \
        --ascat_min_counts 20 \
        --ascat_genome hg38 \
       	--umi_read_structure '9M+T +T' \
	-resume