.RData
.Rhistory
.gitignore
AGENTS.md
Dockerfile
LICENSE
MANIFEST.in
README.md
SampleSheet.csv
alignstats_combo_mqc.tsv
check_popvcf.py
download_presigned.sh
dyoainit
giab_30x_hg38_analysis_manifest.csv
presigned_manifest.tsv
pyproject.toml
setup.py
summary_results.tsv
vcf_inventory.tsv
.ignore/alignstats_PAY87794.sbatch
.ignore/alignstats_PAY87954.sbatch
.ignore/build_chrM_refs.sh
.ignore/commit_msg.txt
.ignore/commit_sr_rg_fix.sh
.ignore/downsample_ont_15xactual.sbatch
.ignore/downsample_ont_20x.sbatch
.ignore/downsample_ont_20x_v2.sbatch
.ignore/fix_chain_blacklist.sh
.ignore/fix_hap_bam_index.sh
.ignore/launch_hiom_fresh.sh
.ignore/monitor_hiomr.sh
.ignore/poll_gatk_full.sh
.ignore/poll_gatk_test.sh
.ignore/restart_hiom.sh
.ignore/restart_huom.sh
.ignore/setup_chrM_refs.sh
bin/_gen_check_cram.py
bin/_gen_check_errs.py
bin/_gen_check_outputs.py
bin/_gen_check_slurm2.py
bin/_gen_check_slurm_logs.py
bin/_gen_check_units.py
bin/_gen_detailed_check.py
bin/_gen_real_validation.py
bin/_gen_status_check.py
bin/_gen_val_rerun.py
bin/_gen_validate.py
bin/_gen_validate_v2.py
bin/addreplacereadgroup.sh
bin/all_zones.csv
bin/augment_setup_and_run_dayoa.bash
bin/build_illumina_read_fate_river.py
bin/calc_benchmark_stats.py
bin/calc_concordance_stats.py
bin/calc_coverage_evenness_two.py
bin/calc_uniq_footprint.py
bin/cat_input_files.sh
bin/check_aws_permissions.sh
bin/check_cram_integrity.sh
bin/check_prereq_sw.sh
bin/create_clinvar_gene_regions_bed.py
bin/day_activate
bin/day_deactivate
bin/day_monitor
bin/day_openai_env.bash
bin/day_run
bin/day_set_genome_build
bin/downsample_cram.sh
bin/fetch_err_sources.py
bin/filter_cram.sh
bin/fix_cram_header_pp_mising_for_ont.sh
bin/gen_bcl2fq_ss.py
bin/gen_experiment_uid.py
bin/get_git_deets.sh
bin/headnode-job-deets.bash
bin/launch_sleepjob_spotinstance.sh
bin/merge_caller_vcfs.bash
bin/monitor_ifx_go.sh
bin/monitor_ifx_go_remote.py
bin/multiqc_ilmn_run_metrics.sh
bin/multiqc_ont_demux_fastq_qc.sh
bin/multiqc_ont_run_metrics.sh
bin/proc_aligner_costs.sh
bin/proc_benchmark_runtime.sh
bin/proc_mrkdup_costs.sh
bin/proc_spot_price_logs.sh
bin/qc_fastq_files_for_read_order_matching.sh
bin/repair_lofreq2_vcf.sh
bin/retshell
bin/rtg_vcfeval_standalone.sh
bin/run_concordance_standalone.sh
bin/sentieon_mitochondrial_pipeline.sh
bin/sinfo-monitor-extended.bash
bin/sleep_test.sh
bin/squeue-monitor-extended.bash
bin/strip_chrms_from_cram.sh
bin/tabcomp.bash
bin/test_sleep.sh
bin/tmp_launch_mod_ug_ont.sh
bin/validate_extensions.sh
bin/validate_extensions_v2.sh
bin/verify_ensemble_integration.sh
bin/helpers/acmg_annotator.py
bin/helpers/annotate_vcf_w_clinvar.py
bin/helpers/common.py
bin/helpers/correlates.py
bin/helpers/dl_grch_ref.py
bin/helpers/fetch_and_index_grch38.py
bin/helpers/fetch_b37_giabvcf.log
bin/helpers/fetch_hg38_giabvcf.log
bin/helpers/gather_conda_tool_citations.py
bin/helpers/giab_locations.fofn
bin/other/regsub_yaml.sh
bin/util/add_sampleid_to_output_summary.sh
bin/util/alignstats_compile.sh
bin/util/cat_basespace_fqs_to_single_r1r2_s3.sh
bin/util/check_headnode_status.sh
bin/util/col_error.bash
bin/util/create_deep_var_model.sh
bin/util/create_deep_var_trainmodel.sh
bin/util/create_downsampled_datasets.py
bin/util/create_pub_ref_bucket.sh
bin/util/downsample_7x_all_platforms.sh
bin/util/downsample_cram_batch.sh
bin/util/downsample_ilmn_fastqs.sh
bin/util/downsample_ont_1x_3x.sh
bin/util/downsample_ont_multi_coverage.sh
bin/util/dump_fastq_from_bam_cram.sh
bin/util/expand_dev_shm.sh
bin/util/extract_40x_50x_fastqs.sh
bin/util/extract_fastq_from_roche_bam.sh
bin/util/extract_fastq_from_ultima_cram.sh
bin/util/fix_ont_cram_headers.sh
bin/util/fix_ultima_cram_headers.sh
bin/util/fix_ultima_multi_coverage.sh
bin/util/gatk_cram_compat.sh
bin/util/generate_downsample_series_manifests.py
bin/util/genotype_free_contam_estimator.py
bin/util/launch_1x_3x_all_workflows.sh
bin/util/make_giab_hg002_hg003_contam_fastqs.py
bin/util/merge_downsample_ont_combined.sh
bin/util/parse_expansionhunter_json.py
bin/util/plot_concord_data.r
bin/util/profile_freshness_warn.bash
bin/util/restart_ilmn_deep19_fix.sh
bin/util/restart_ilmn_solo.sh
bin/util/run_all_dragen.sh
bin/util/shfmt
bin/util/shuffle_training.sh
bin/util/shuffle_validation.sh
bin/util/simple_subsample.py
bin/util/stage_hprc_pangenome_resources.sh
bin/util/summarize_contamination_expected_vs_observed.py
bin/util/summarize_proc_times.sh
bin/util/user_pays.json
bin/util/write_peddy_low_data_outputs.py
bin/util/benchmarks/collect_day_benchmark_data.sh
bin/util/benchmarks/concordance_happy_pangenome.smk
bin/util/benchmarks/split_bench_rule_col.py
bin/util/other/fetch_smn12_sample_fqs.sh
bin/util/other/fqfetch.sh
bin/util/other/fqfetch_30x.sh
bin/util/other/smn12_samples_one.md
bin/util/other/smn12_samples_two.md
bin/util/other/smn1_smn2_copy_numbers.tsv
bin/util/other/smn1_smn2_copy_numbers_expanded.tsv
bin/util/other/smn_Callers.pdf
bin/util/other/smn_fetch_table.tsv
bin/util/other/smn_full_table.csv
bin/util/other/smn_samples_extended.csv
bin/util/other/wget_par.sh
config/daylily_cli_global.yaml
config/daylily_ephemeral_cluster.yaml
config/daylily_ephemeral_cost_config.yaml
config/global.yaml
config/global_AWSPC.yaml
config/multiqc_module_exclude.txt
config/relatedness.yaml
config/workflow_target_aliases.tsv
config/cli/colr_themes.sh
config/day/conda_base.yaml
config/day/day.yaml
config/day/day_env_installer.sh
config/day/daycli.yaml
config/day/env.sh
config/day_examples/bcl2fq/bcl2fastq_samplesheet.csv
config/day_examples/bcl2fq/warning.md
config/day_examples/downsample_manifest/subsample_samples_in_manifest.csv
config/day_examples/remoteBAMmanifest/remote_bam_manifest.csv
config/day_examples/vanilla_analysis_manifest/README.md
config/day_examples/vanilla_analysis_manifest/analysis_manifest_running_cocord_on_pos_ctrl.conf
config/day_examples/vanilla_analysis_manifest/rclone_local_example.conf
config/day_examples/vanilla_analysis_manifest/addl_feat_examples/0.01xwgs_NA24694.samplesheet.csv
config/day_examples/vanilla_analysis_manifest/addl_feat_examples/0.1xwgs_NA24694.samplesheet.csv
config/day_examples/vanilla_analysis_manifest/addl_feat_examples/1x_NA24694_samplesheet.csv
config/day_examples/vanilla_analysis_manifest/addl_feat_examples/2x0.1xwgs_NA24694.samplesheet.csv
config/day_examples/vanilla_analysis_manifest/addl_feat_examples/WGSfull_NA12878_samplesheet.csv
config/day_examples/vanilla_analysis_manifest/addl_feat_examples/bcl2fq_samps_fake.csv
config/day_examples/vanilla_analysis_manifest/addl_feat_examples/iddna_test_samplesheet.csv
config/day_examples/vanilla_analysis_manifest/addl_feat_examples/subset_giab_samples_from_wgs_validation.csv
config/day_profiles/local/.hold
config/day_profiles/local/templates/config.yaml
config/day_profiles/local/templates/profile.info
config/day_profiles/local/templates/profile_env.bash
config/day_profiles/local/templates/rule_config.yaml
config/day_profiles/slurm/.hold
config/day_profiles/slurm/templates/config.yaml
config/day_profiles/slurm/templates/profile.info
config/day_profiles/slurm/templates/profile_env.bash
config/day_profiles/slurm/templates/rule_config.yaml
config/day_profiles/slurm/templates/status-scontrols.sh
config/daycli/DAYCLI.yaml
config/external_tools/.rcc.conf
config/external_tools/multiqc.css
config/external_tools/multiqc_config.yaml
config/external_tools/multiqc_header.yaml
config/quickmer2/README.md
config/quickmer2/example_kmers.tsv
config/quickmer2/example_normalization.tsv
config/supporting_files/b37_supporting_files.yaml
config/supporting_files/hg38_broad_supporting_files.yaml
config/supporting_files/hg38_supporting_files.yaml
config/supporting_files/supporting_dirs.yaml
dags/.hold
daylily_omics_analysis/__init__.py
daylily_omics_analysis/evidence_manifest.py
daylily_omics_analysis/pipeline_reports.py
daylily_omics_analysis/workflow_catalog.py
daylily_omics_analysis.egg-info/PKG-INFO
daylily_omics_analysis.egg-info/SOURCES.txt
daylily_omics_analysis.egg-info/dependency_links.txt
daylily_omics_analysis.egg-info/top_level.txt
daylily_omics_analysis/data/workflow_catalog.v1.json
docker/surveyor/Dockerfile
docs/README.md
docs/catalog_of_tools.md
docs/examples/multiqc/README.md
docs/ops/dycli.md
docs/ops/multiqc_qc_targets.md
docs/plans/20260518_day_run_version_publish_ledger.md
docs/plans/20260518_html_report_publish_ledger.md
docs/plans/20260518_mosdepth_metagenomics_workflow_robustness_ledger.md
docs/plans/20260519T063737Z_snakemake_reserved_module_hotfix_ledger.md
docs/plans/20260523T113105Z_ont_solo_full_coverage_release_rerun_ledger.md
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workflow/envs/gba_v0.1.yaml
workflow/envs/genetocn_v0.1.yaml
workflow/envs/go_left_v0.1.yaml
workflow/envs/haplocheck_v0.1.yaml
workflow/envs/hisat2_v0.1.yaml
workflow/envs/kat_v0.1.yaml
workflow/envs/lofreq2_v0.1.yaml
workflow/envs/longtr_v0.1.yaml
workflow/envs/manta_uge_v0.2.yaml
workflow/envs/manta_v0.1.yaml
workflow/envs/mosdepth_v0.1.yaml
workflow/envs/multiqc_v0.1.yaml
workflow/envs/ngstroublefinder_v0.1.yaml
workflow/envs/octopus_v0.7.yaml
workflow/envs/pangenome_ultima_v0.1.yaml
workflow/envs/parascopy_v0.1.yaml
workflow/envs/peddy.yaml
workflow/envs/peddy_v0.1.yaml
workflow/envs/picard.yaml
workflow/envs/picard_v0.1.yaml
workflow/envs/prep_input_sample_files_v0.1.yaml
workflow/envs/qualimap_v0.1.yaml
workflow/envs/quickmer2_v0.1.yaml
workflow/envs/read_haps_v0.1.yaml
workflow/envs/report.yaml
workflow/envs/roche_v0.1.yaml
workflow/envs/rtgtools_v0.1.yaml
workflow/envs/run_qc_reports_v0.1.yaml
workflow/envs/sambamba_v0.1.yaml
workflow/envs/samtools_v0.1.yaml
workflow/envs/segdup_v0.1.yaml
workflow/envs/sentD_v0.2.yaml
workflow/envs/sent_pangenome_v0.1.yaml
workflow/envs/sentieonHybrid_v0.1.yaml
workflow/envs/sentieon_gatk_v0.1.yaml
workflow/envs/sentieon_v0.1.yaml
workflow/envs/sentieon_v0.2b.yaml
workflow/envs/sentieon_v0.3.yaml
workflow/envs/sentieon_v0.3b.yaml
workflow/envs/sentmm2_v0.1.yaml
workflow/envs/sentmm2ont_v0.1.yaml
workflow/envs/site_mix_contam_v0.1.yaml
workflow/envs/smaca_v0.1.yaml
workflow/envs/smn12_v0.1.yaml
workflow/envs/snpeff_v0.1.yaml
workflow/envs/somalier.yaml
workflow/envs/stargazer_v0.1.yaml
workflow/envs/strobe_aligner.yaml
workflow/envs/surveyor_v0.1.yaml
workflow/envs/svim_asm_v0.1.yaml
workflow/envs/tiddit_v0.1.yaml
workflow/envs/truvari_v0.1.yaml
workflow/envs/unmapped_metagenomics_ganon2_v0.1.yaml
workflow/envs/unmapped_metagenomics_sourmash_v0.1.yaml
workflow/envs/unmapped_metagenomics_v0.1.yaml
workflow/envs/vanilla_v0.1.yaml
workflow/envs/verifybamid2_v0.1.yaml
workflow/envs/vpot_v0.1.yaml
workflow/report/workflow.rst
workflow/rules/aivariant.smk
workflow/rules/align_from_bam.smk
workflow/rules/alignstats.smk
workflow/rules/alignstats_compile.smk
workflow/rules/art.smk
workflow/rules/bcftools_vcfstat.smk
workflow/rules/bcl2fq.smk
workflow/rules/bclconvert.smk
workflow/rules/benchmarks.smk
workflow/rules/bwa_mem2a_align_sort.smk
workflow/rules/calc_coverage_eveness.smk
workflow/rules/calc_coverage_evenness_two.smk
workflow/rules/clair3.smk
workflow/rules/clair3s_to.smk
workflow/rules/common.smk
workflow/rules/contam_identity.smk
workflow/rules/cyp2d6_cyrius.smk
workflow/rules/deepsomatic.smk
workflow/rules/deepvariant_1_5.smk
workflow/rules/deepvariant_1_9.smk
workflow/rules/deepvariant_1_9_roche.smk
workflow/rules/deepvariant_ug.smk
workflow/rules/doppel_mrkdups.smk
workflow/rules/duphold.smk
workflow/rules/dysgu_sv.smk
workflow/rules/evidence_manifest.smk
workflow/rules/expansionhunter.smk
workflow/rules/fastp.smk
workflow/rules/fastqc.smk
workflow/rules/gatk_contam.smk
workflow/rules/gauchian.smk
workflow/rules/generate_deduplicated_bams.smk
workflow/rules/genetocn.smk
workflow/rules/global_common.smk
workflow/rules/go_left.smk
workflow/rules/hap2.sh
workflow/rules/help.smk
workflow/rules/hisat2.smk
workflow/rules/htd_calls.smk
workflow/rules/hyb_ensemble_multi_platform.smk
workflow/rules/kat.smk
workflow/rules/legacy_cram_compat_bam.smk
workflow/rules/lofreq2.smk
workflow/rules/longtr.smk
workflow/rules/manta.smk
workflow/rules/merge_all_bams.smk
workflow/rules/mosdepth.smk
workflow/rules/multiqc_cov_aln.smk
workflow/rules/multiqc_final_wgs.smk
workflow/rules/multiqc_for_bcl2fq.smk
workflow/rules/multiqc_for_raw_fastqs.smk
workflow/rules/multiqc_singleton.smk
workflow/rules/mutect2.smk
workflow/rules/no_dedup.smk
workflow/rules/no_dedup_cram.smk
workflow/rules/octopus.smk
workflow/rules/parascopy.smk
workflow/rules/peddy.smk
workflow/rules/picard.smk
workflow/rules/prep_input_sample_files.smk
workflow/rules/proc_dragen.smk
workflow/rules/produce_fastq_from_bams.smk
workflow/rules/qualimap.smk
workflow/rules/quickmer2.smk
workflow/rules/relatedness_batch.smk
workflow/rules/relatedness_test_day.smk
workflow/rules/roche_sbxd.smk
workflow/rules/rtg_vcfeval.smk
workflow/rules/rtg_vcfstats.smk
workflow/rules/run_qc_reports.smk
workflow/rules/samtools_metrics.smk
workflow/rules/sent_DNAscope.smk
workflow/rules/sent_DNAscope_cgt7p.smk
workflow/rules/sent_TNscope.smk
workflow/rules/sent_aln_sort_snv.smk
workflow/rules/sent_hybrid_ilmn_ont_modular.refactored.smk
workflow/rules/sent_hybrid_ilmn_pb_modular.refactored.smk
workflow/rules/sent_hybrid_ug_ont_modular.refactored.smk
workflow/rules/sent_hybrid_ug_pb_modular.refactored.smk
workflow/rules/sent_snv_ont.smk
workflow/rules/sent_snv_pb.smk
workflow/rules/sent_snv_ug.smk
workflow/rules/sentieon.smk
workflow/rules/sentieon_gatk.smk
workflow/rules/sentieon_markdups.smk
workflow/rules/sentieon_new_gatk.smk
workflow/rules/sentieon_pangenome_shortreads.smk
workflow/rules/sentieon_pangenome_ug.smk
workflow/rules/sentmm2_align_sort.smk
workflow/rules/sentmm2ont_align_sort.smk
workflow/rules/seqfu.smk
workflow/rules/seqtk_subsamplefq.smk
workflow/rules/site_mix_contam.smk
workflow/rules/smaca.smk
workflow/rules/smn_copynumbercaller.smk
workflow/rules/snpeff.smk
workflow/rules/stargazer.smk
workflow/rules/strelka2.smk
workflow/rules/strobe_align_sort.smk
workflow/rules/supporting_data.smk
workflow/rules/surveyor.smk
workflow/rules/test_cluster_job.smk
workflow/rules/tiddit.smk
workflow/rules/truvari_sv_benchmark.smk
workflow/rules/unmapped_metagenomics.smk
workflow/rules/varnet.smk
workflow/rules/vep.smk
workflow/rules/vpot.smk
workflow/rules/workflow_staging.smk
workflow/rules/workflow_target_aliases.smk
workflow/rules/archived_qc/fastv.smk
workflow/rules/archived_qc/verifybamid2_contam.smk
workflow/rules/explore/str_spy.smk
workflow/rules/explore/svaba.smk
workflow/rules/explore/svim_asm.smk
workflow/rules/explore/svlib.smk
workflow/rules/to-deprecate/sent_hybrid_ilmn_ont.smk
workflow/rules/to-deprecate/sent_hybrid_ilmn_ont_modular.smk
workflow/rules/to-deprecate/sent_hybrid_ilmn_pb.smk
workflow/rules/to-deprecate/sent_hybrid_ilmn_pb_modular.smk
workflow/rules/to-deprecate/sent_hybrid_roche_ont_modular.smk
workflow/rules/to-deprecate/sent_hybrid_roche_pb_modular.smk
workflow/rules/to-deprecate/sent_hybrid_ug_ont.smk
workflow/rules/to-deprecate/sent_hybrid_ug_ont_modular.smk
workflow/rules/to-deprecate/sent_hybrid_ug_pb.smk
workflow/rules/to-deprecate/sent_hybrid_ug_pb_modular.smk
workflow/rules/to_conv_from_bam_to_cram/paragraph.smk
workflow/schemas/analysis_manifest.schema.yaml
workflow/schemas/config.schema.yaml
workflow/schemas/global.schema.yaml
workflow/schemas/samples.schema.yaml
workflow/schemas/supporting_dirs_schema.yaml
workflow/schemas/units.schema.yaml
workflow/scripts/bclconvert_fastq_list_to_units.py
workflow/scripts/bclconvert_metrics_summary.py
workflow/scripts/bclconvert_metrics_to_multiqc.py
workflow/scripts/buid_conc_cmds.sh
workflow/scripts/calc_norm_cov_sd.R
workflow/scripts/calc_norm_cov_sd_2.R
workflow/scripts/classify_var_by_type_size.py
workflow/scripts/compile_alignstats.py
workflow/scripts/compile_contam_identity_mqc.py
workflow/scripts/compile_contamination_mqc.py
workflow/scripts/convert_expansionhunter_catalog_to_longtr_bed.py
workflow/scripts/fastq_path_lists.py
workflow/scripts/force_multiqc_dark_mode.py
workflow/scripts/htd_calls_mqc.py
workflow/scripts/illumina_run_qc_to_multiqc.py
workflow/scripts/input_sample_libraries_mqc.py
workflow/scripts/link_source_fqs.py
workflow/scripts/make_scoped_diploid_bed.py
workflow/scripts/manta_uniter.py
workflow/scripts/multiqc_custom_output_inventory.py
workflow/scripts/multiqc_log_guard.py
workflow/scripts/multiqc_module_exclude_args.py
workflow/scripts/parse-vcfeval-summary.py
workflow/scripts/parse_bclconvert_samplesheet.py
workflow/scripts/parse_truvari_summary.py
workflow/scripts/relatedness_report.py
workflow/scripts/run_charr_contam.py
workflow/scripts/sort_concat_chrm_list.py
workflow/scripts/stage_multiqc_inputs.py
workflow/scripts/summarize_run_qc_report.py
workflow/scripts/summarize_unmapped_ganon2.py
workflow/scripts/summarize_unmapped_metagenomics.py
workflow/scripts/summarize_unmapped_sourmash.py
workflow/scripts/tiddit_sv_to_multiqc.py
workflow/scripts/validate_multiqc_sample_ids.py
workflow/scripts/write_dayoa_evidence_manifest.py
workflow/scripts/write_illumina_run_qc_json.py
workflow/scripts/write_interop_summary_csv.py