bin/day_run produce_sentdhiomr_snv_vcf produce_snv_concordances produce_sentdhiomr_sv produce_tiddit_sv_vcf produce_sentdhiomr_cnv produce_sentdhiomr_segdup produce_sentdhiomr_mito produce_expansionhunter produce_alignstats produce_relatedness produce_peddy produce_gatk_contam_estimate produce_site_mix_contam_estimate produce_vep produce_htd_calls produce_smn12_orthogonal_calls produce_metagenomics produce_multiqc_all results/day/hg38/reports/DAY_final_multiqc.html results/day/hg38/reports/dayoa_evidence_manifest.json --config 'aligners=["sent"]' 'dedupers=["na"]' 'snv_callers=["sentdhiomr"]' 'sv_callers=["sentdhiomr","tiddit"]' 'sentdhiomr={"segdup_genes":"SMN1"}' 'htd_callers=["smn12"]' 'multiqc_qc={"enable_tools":["vep","unmapped_metagenomics_ganon2","gatk_contam","site_mix","peddy"]}' -j 250 -p -T 0 --rerun-triggers mtime --rerun-incomplete --produce-ursa-manifest true --produce-rulegraph true --produce-filegraph false --produce-dag false
