Example run command:
nextflow run main.nf --reference_fasta /expanse/lustre/projects/ddp195/eiovino/fasta/Homo_sapiens_assembly38.fasta \
--sample_alignments_tsv input_REACH2.csv --outdir /expanse/lustre/projects/ddp195/eiovino/sv_pipeline_nf/SV_result_REACH/REACH_cohort \
--delly_exclude_regions_bed data/exlude.regions.delly.human.hg38.excl.tsv \
--smoove_exclude_regions_bed data/exclude.smoove.cnvnator_100bp.GRCh38.20170403.bed \
--expansion_hunter_variant_catalog_json Hg38/ExpansioHunter_variant_catalog.json \
--recode_delly_python_script data/recode_delly.py \
--mosdepth_segmental_duplications_bed data/Segmental_dups_hg38_frt_srt.bed \
--bind_path /expanse/lustre/projects/ddp195/eiovino/sv_pipeline_nf,/expanse/lustre/projects/ddp195/eiovino/fasta,/expanse/lustre/projects/ddp195/eiovino/test_pipeline/Sv_pipeline/data,/expanse/lustre/projects/ddp195/eiovino/test_pipeline/Sv_pipeline/Hg38,/expanse/projects/sebat1/genomicsdataanalysis/REACH_MSSNG/request_202001/ \
-profile slurm \
-resume