{
  "command_catalog_version": 2,
  "commands": [
    {
      "aligners": [],
      "artifact_registration": null,
      "command_class": "utility",
      "command_id": "simple-test",
      "compatible_data_modes": [
        "none"
      ],
      "compatible_platforms": [
        "local"
      ],
      "datasource": "DayOA",
      "dedupers": [],
      "description": "Smoke-test DayOA shell initialization and local help target without staged sample inputs.",
      "display_name": "Simple Test",
      "dryrun_dy_command": "source dyoainit; dy-a local hg38; dy-r -p -k -j 1 help",
      "dy_command": "source dyoainit; dy-a local hg38; dy-r -p -k -j 1 help",
      "genome": "hg38",
      "git_tag": "2.0.23",
      "input_contract": "none",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {},
        "required_source_columns": []
      },
      "jobs": 1,
      "launcher": "workflow_launch",
      "no_containerized": true,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": false,
      "runtime_parameters": {},
      "snv_callers": [],
      "sv_callers": [],
      "targets": [
        "help"
      ],
      "validation_runs": []
    },
    {
      "aligners": [
        "sent"
      ],
      "artifact_registration": null,
      "command_class": "sample_analysis",
      "command_id": "illumina_snv_alignstats",
      "compatible_data_modes": [
        "ilmn_solo"
      ],
      "compatible_platforms": [
        "ILMN"
      ],
      "datasource": "Illumina",
      "dedupers": [
        "dmd"
      ],
      "description": "Illumina WGS Sentieon DNAscope and alignment-statistics launch profile.",
      "display_name": "Illumina SNV + Alignstats",
      "dryrun_dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_snv_concordances produce_alignstats -p -k -j 20 -n",
      "dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_snv_concordances produce_alignstats -p -k -j 20",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {},
        "required_source_columns": [
          "ILMN_R1_FQ",
          "ILMN_R2_FQ"
        ]
      },
      "jobs": 20,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "sentd"
      ],
      "sv_callers": [],
      "targets": [
        "produce_sent_align",
        "produce_dmd_dedup_cram",
        "produce_sentd_snv_vcf",
        "produce_snv_concordances",
        "produce_alignstats"
      ],
      "validation_runs": [
        {
          "cluster": "tstVer4-1-1b",
          "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
          "dayec_tag": "4.1.3",
          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
          "dayoa_tag": "1.0.21",
          "dryrun_analysis_id": "tvb_illumina_snv_alignstats_5x_1021_dryrun",
          "dryrun_status": "success",
          "failure_cause": "",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "tvb_illumina_snv_alignstats_5x_1021",
          "live_status": "success",
          "notes": "Live run completed with CRAM, VCF, alignstats, and concordance outputs.",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T071517Z",
          "status": "success",
          "tested_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_snv_concordances produce_alignstats -p -k -j 20"
        }
      ]
    },
    {
      "aligners": [
        "sent"
      ],
      "artifact_registration": {
        "enabled": true,
        "evidence_manifest_path": "results/day/{genome}/reports/dayoa_evidence_manifest.json",
        "identity": {
          "analysis_euid": "{analysis_id}",
          "assay_id": "",
          "project_euid": "",
          "run_euid": "{analysis_id}",
          "workset_euid": ""
        },
        "include_classifications": [
          "multiqc_html",
          "multiqc_data_json",
          "multiqc_general_stats",
          "multiqc_sources",
          "multiqc_log",
          "custom_mqc_tsv",
          "staging_manifest",
          "benchmark"
        ],
        "include_paths": [
          "results/day/{genome}/reports/DAY_final_multiqc.html",
          "results/day/{genome}/reports/DAY_final_multiqc_data/**",
          "results/day/{genome}/reports/multiqc_inputs/final/manifest.tsv",
          "results/day/{genome}/other_reports/*_mqc.tsv"
        ],
        "multiqc_report_kind": "final",
        "multiqc_version": "1.35",
        "parser_family_hint": "multiqc",
        "require_existing": true
      },
      "command_class": "sample_analysis",
      "command_id": "illumina_snv_alignstats_relatedness_vep_multiqc",
      "compatible_data_modes": [
        "ilmn_solo"
      ],
      "compatible_platforms": [
        "ILMN"
      ],
      "datasource": "Illumina",
      "dedupers": [
        "dmd"
      ],
      "description": "Illumina WGS Sentieon DNAscope, alignment statistics, relatedness, VEP annotation, and final MultiQC launch profile.",
      "display_name": "Illumina SNV + Alignstats + Relatedness + VEP MultiQC",
      "dryrun_dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k -n",
      "dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {},
        "required_source_columns": [
          "ILMN_R1_FQ",
          "ILMN_R2_FQ"
        ]
      },
      "jobs": 100,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "sentd"
      ],
      "sv_callers": [],
      "targets": [
        "produce_sent_align",
        "produce_dmd_dedup_cram",
        "produce_sentd_snv_vcf",
        "produce_alignstats",
        "produce_snv_concordances",
        "produce_relatedness",
        "produce_vep",
        "produce_multiqc_all"
      ],
      "validation_runs": [
        {
          "cluster": "tstVer4-1-1b",
          "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
          "dayec_tag": "4.1.3",
          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
          "dayoa_tag": "1.0.21",
          "dryrun_analysis_id": "tvb_illumina_related_vep_multiqc_5x_1021_dryrun",
          "dryrun_status": "success",
          "failure_cause": "",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "tvb_illumina_related_vep_multiqc_5x_1021",
          "live_status": "success",
          "notes": "Live run completed with CRAM, VCF, alignstats, concordance, MultiQC, and relatedness outputs.",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T072540Z",
          "status": "success",
          "tested_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k"
        }
      ]
    },
    {
      "aligners": [
        "sent"
      ],
      "artifact_registration": {
        "enabled": true,
        "evidence_manifest_path": "results/day/{genome}/reports/dayoa_evidence_manifest.json",
        "identity": {
          "analysis_euid": "{analysis_id}",
          "assay_id": "",
          "project_euid": "",
          "run_euid": "{analysis_id}",
          "workset_euid": ""
        },
        "include_classifications": [
          "multiqc_html",
          "multiqc_data_json",
          "multiqc_general_stats",
          "multiqc_sources",
          "multiqc_log",
          "custom_mqc_tsv",
          "staging_manifest",
          "benchmark"
        ],
        "include_paths": [
          "results/day/{genome}/reports/DAY_final_multiqc.html",
          "results/day/{genome}/reports/DAY_final_multiqc_data/**",
          "results/day/{genome}/reports/multiqc_inputs/final/manifest.tsv",
          "results/day/{genome}/other_reports/*_mqc.tsv"
        ],
        "multiqc_report_kind": "final",
        "multiqc_version": "1.35",
        "parser_family_hint": "multiqc",
        "require_existing": true
      },
      "command_class": "sample_analysis",
      "command_id": "illumina_hg002_kitchensink_multiqc",
      "compatible_data_modes": [
        "ilmn_solo"
      ],
      "compatible_platforms": [
        "ILMN"
      ],
      "datasource": "Illumina",
      "dedupers": [
        "dmd"
      ],
      "description": "HG002 Illumina WGS Sentieon DNAscope, dmd CRAM, concordance, relatedness, contamination identity, VEP, ExpansionHunter, HTD, metagenomics, and final MultiQC validation profile.",
      "display_name": "Illumina HG002 Kitchen Sink MultiQC",
      "dryrun_dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_gatk_contam_estimate produce_site_mix_contam_estimate produce_global_contam_check produce_vep produce_expansionhunter produce_htd_calls produce_metagenomics produce_multiqc_all --config 'aligners=[\"sent\"]' 'dedupers=[\"dmd\"]' 'snv_callers=[\"sentd\"]' 'htd_callers=[\"cyrius\"]' 'multiqc_qc={\"enable_tools\":[\"vep\",\"metagenomics\",\"contam_identity\"]}' -j 200 -p -k --rerun-triggers mtime -n",
      "dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_gatk_contam_estimate produce_site_mix_contam_estimate produce_global_contam_check produce_vep produce_expansionhunter produce_htd_calls produce_metagenomics produce_multiqc_all --config 'aligners=[\"sent\"]' 'dedupers=[\"dmd\"]' 'snv_callers=[\"sentd\"]' 'htd_callers=[\"cyrius\"]' 'multiqc_qc={\"enable_tools\":[\"vep\",\"metagenomics\",\"contam_identity\"]}' -j 200 -p -k --rerun-triggers mtime",
      "genome": "hg38",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {},
        "required_source_columns": [
          "ILMN_R1_FQ",
          "ILMN_R2_FQ"
        ]
      },
      "jobs": 200,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "sentd"
      ],
      "sv_callers": [],
      "targets": [
        "produce_sent_align",
        "produce_dmd_dedup_cram",
        "produce_sentd_snv_vcf",
        "produce_alignstats",
        "produce_snv_concordances",
        "produce_relatedness",
        "produce_gatk_contam_estimate",
        "produce_site_mix_contam_estimate",
        "produce_global_contam_check",
        "produce_vep",
        "produce_expansionhunter",
        "produce_htd_calls",
        "produce_metagenomics",
        "produce_multiqc_all"
      ],
      "validation_runs": [
        {
          "cluster": "goodole3",
          "dayec_commit": "fbad3b802f2886afdc011d41228c12a1b9094322",
          "dayec_tag": "5.0.20-dev",
          "dayoa_commit": "b377b8b557306fbb6832763a39661ce36d6f4bbd",
          "dayoa_tag": "2.0.19",
          "dryrun_analysis_id": "dayoa_2017_hg002_kitchensink_j200_readhapsfix2_151101_dryrun",
          "dryrun_status": "success",
          "failure_cause": "",
          "generated_at": "2026-05-28T15:11:45Z",
          "ledger_path": "docs/plans/20260528T152607Z_dayoa_2017_release_train_ledger.md",
          "live_analysis_id": "dayoa_2017_hg002_kitchensink_j200_readhapsfix2_151101",
          "live_status": "success",
          "notes": "Headnode run used the dy-r alias with the same targets/config on the 2.0.17 clone plus local stabilization patches that were mirrored into DayOA release 2.0.19; final report was results/day/hg38/reports/DAY_final_multiqc.html.",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/plans/20260528T152607Z_dayoa_2017_release_train_ledger.md",
          "run_id": "dayoa_2017_hg002_kitchensink_j200_readhapsfix2_151101",
          "stage_or_context": "/fsx/analysis_results/ubuntu/2.0.17/daylily-omics-analysis",
          "status": "success",
          "tested_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_gatk_contam_estimate produce_site_mix_contam_estimate produce_global_contam_check produce_vep produce_expansionhunter produce_htd_calls produce_metagenomics produce_multiqc_all --config 'aligners=[\"sent\"]' 'dedupers=[\"dmd\"]' 'snv_callers=[\"sentd\"]' 'htd_callers=[\"cyrius\"]' 'multiqc_qc={\"enable_tools\":[\"vep\",\"metagenomics\",\"contam_identity\"]}' -j 200 -p -k --rerun-triggers mtime"
        }
      ]
    },
    {
      "aligners": [
        "ug"
      ],
      "artifact_registration": null,
      "command_class": "sample_analysis",
      "command_id": "ultima_snv_alignstats",
      "compatible_data_modes": [
        "ultima_solo"
      ],
      "compatible_platforms": [
        "ULTIMA"
      ],
      "datasource": "Ultima",
      "dedupers": [
        "na"
      ],
      "description": "Ultima CRAM/FASTQ Sentieon DNAscope and alignment-statistics launch profile.",
      "display_name": "Ultima SNV + Alignstats",
      "dryrun_dy_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_sentdug_snv_vcf produce_snv_concordances -p -j 20 -k -n",
      "dy_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_sentdug_snv_vcf produce_snv_concordances -p -j 20 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [
          [
            "UG_R1_FQ",
            "UG_R2_FQ"
          ],
          [
            "ULTIMA_CRAM",
            "ULTIMA_CRAM_ALIGNER",
            "ULTIMA_CRAM_SNV_CALLER"
          ]
        ],
        "required_run_context_values": {},
        "required_source_columns": []
      },
      "jobs": 20,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "sentdug"
      ],
      "sv_callers": [],
      "targets": [
        "produce_alignstats",
        "produce_na_dedup_cram",
        "produce_sentdug_snv_vcf",
        "produce_snv_concordances"
      ],
      "validation_runs": [
        {
          "cluster": "tstVer4-1-1b",
          "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
          "dayec_tag": "4.1.3",
          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
          "dayoa_tag": "1.0.21",
          "dryrun_analysis_id": "tvb_ultima_snv_alignstats_5x_1021_dryrun",
          "dryrun_status": "success",
          "failure_cause": "",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "tvb_ultima_snv_alignstats_5x_1021",
          "live_status": "success",
          "notes": "Live run completed with VCF, alignstats, and concordance outputs.",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T072907Z",
          "status": "success",
          "tested_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_sentdug_snv_vcf produce_snv_concordances -p -j 20 -k"
        }
      ]
    },
    {
      "aligners": [
        "ug"
      ],
      "artifact_registration": {
        "enabled": true,
        "evidence_manifest_path": "results/day/{genome}/reports/dayoa_evidence_manifest.json",
        "identity": {
          "analysis_euid": "{analysis_id}",
          "assay_id": "",
          "project_euid": "",
          "run_euid": "{analysis_id}",
          "workset_euid": ""
        },
        "include_classifications": [
          "multiqc_html",
          "multiqc_data_json",
          "multiqc_general_stats",
          "multiqc_sources",
          "multiqc_log",
          "custom_mqc_tsv",
          "staging_manifest",
          "benchmark"
        ],
        "include_paths": [
          "results/day/{genome}/reports/DAY_final_multiqc.html",
          "results/day/{genome}/reports/DAY_final_multiqc_data/**",
          "results/day/{genome}/reports/multiqc_inputs/final/manifest.tsv",
          "results/day/{genome}/other_reports/*_mqc.tsv"
        ],
        "multiqc_report_kind": "final",
        "multiqc_version": "1.35",
        "parser_family_hint": "multiqc",
        "require_existing": true
      },
      "command_class": "sample_analysis",
      "command_id": "ultima_snv_alignstats_kitchensink",
      "compatible_data_modes": [
        "ultima_solo"
      ],
      "compatible_platforms": [
        "ULTIMA"
      ],
      "datasource": "Ultima",
      "dedupers": [
        "na"
      ],
      "description": "Ultima CRAM/FASTQ Sentieon DNAscope, alignment statistics, relatedness, VEP annotation, and final MultiQC launch profile.",
      "display_name": "Ultima SNV + Alignstats Kitchen Sink",
      "dryrun_dy_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_sentdug_snv_vcf produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k -n",
      "dy_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_sentdug_snv_vcf produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [
          [
            "UG_R1_FQ",
            "UG_R2_FQ"
          ],
          [
            "ULTIMA_CRAM",
            "ULTIMA_CRAM_ALIGNER",
            "ULTIMA_CRAM_SNV_CALLER"
          ]
        ],
        "required_run_context_values": {},
        "required_source_columns": []
      },
      "jobs": 100,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "sentdug"
      ],
      "sv_callers": [],
      "targets": [
        "produce_alignstats",
        "produce_na_dedup_cram",
        "produce_sentdug_snv_vcf",
        "produce_snv_concordances",
        "produce_relatedness",
        "produce_vep",
        "produce_multiqc_all"
      ],
      "validation_runs": []
    },
    {
      "aligners": [
        "ont"
      ],
      "artifact_registration": null,
      "command_class": "sample_analysis",
      "command_id": "ont_snv_alignstats",
      "compatible_data_modes": [
        "ont_solo"
      ],
      "compatible_platforms": [
        "ONT"
      ],
      "datasource": "ONT",
      "dedupers": [
        "na"
      ],
      "description": "ONT alignment, Sentieon DNAscope, and alignment-statistics launch profile.",
      "display_name": "ONT SNV + Alignstats",
      "dryrun_dy_command": "bin/day_run produce_alignstats produce_sentdont_snv_vcf produce_snv_concordances -p -j 5 -k -n",
      "dy_command": "bin/day_run produce_alignstats produce_sentdont_snv_vcf produce_snv_concordances -p -j 5 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [
          [
            "ONT_R1_FQ",
            "ONT_R2_FQ"
          ],
          [
            "ONT_FASTQ_PREFIX"
          ],
          [
            "ONT_CRAM",
            "ONT_CRAM_ALIGNER",
            "ONT_CRAM_SNV_CALLER"
          ],
          [
            "ONT_BAM",
            "ONT_BAM_ALIGNER",
            "ONT_BAM_SNV_CALLER"
          ]
        ],
        "required_run_context_values": {},
        "required_source_columns": []
      },
      "jobs": 5,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "sentdont"
      ],
      "sv_callers": [],
      "targets": [
        "produce_alignstats",
        "produce_sentdont_snv_vcf",
        "produce_snv_concordances"
      ],
      "validation_runs": [
        {
          "cluster": "tstVer4-1-1b",
          "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
          "dayec_tag": "4.1.3",
          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
          "dayoa_tag": "1.0.21",
          "dryrun_analysis_id": "tvb_ont_snv_alignstats_5x_1021_dryrun",
          "dryrun_status": "success",
          "failure_cause": "",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "tvb_ont_snv_alignstats_5x_1021",
          "live_status": "success",
          "notes": "Live run completed with VCF, alignstats, and concordance outputs.",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T073112Z",
          "status": "success",
          "tested_command": "bin/day_run produce_alignstats produce_sentdont_snv_vcf produce_snv_concordances -p -j 5 -k"
        }
      ]
    },
    {
      "aligners": [
        "ont"
      ],
      "artifact_registration": {
        "enabled": true,
        "evidence_manifest_path": "results/day/{genome}/reports/dayoa_evidence_manifest.json",
        "identity": {
          "analysis_euid": "{analysis_id}",
          "assay_id": "",
          "project_euid": "",
          "run_euid": "{analysis_id}",
          "workset_euid": ""
        },
        "include_classifications": [
          "multiqc_html",
          "multiqc_data_json",
          "multiqc_general_stats",
          "multiqc_sources",
          "multiqc_log",
          "custom_mqc_tsv",
          "staging_manifest",
          "benchmark"
        ],
        "include_paths": [
          "results/day/{genome}/reports/DAY_final_multiqc.html",
          "results/day/{genome}/reports/DAY_final_multiqc_data/**",
          "results/day/{genome}/reports/multiqc_inputs/final/manifest.tsv",
          "results/day/{genome}/other_reports/*_mqc.tsv"
        ],
        "multiqc_report_kind": "final",
        "multiqc_version": "1.35",
        "parser_family_hint": "multiqc",
        "require_existing": true
      },
      "command_class": "sample_analysis",
      "command_id": "ont_snv_alignstats_kitchensink",
      "compatible_data_modes": [
        "ont_solo"
      ],
      "compatible_platforms": [
        "ONT"
      ],
      "datasource": "ONT",
      "dedupers": [
        "na"
      ],
      "description": "ONT alignment, Sentieon DNAscope, alignment statistics, relatedness, VEP annotation, and final MultiQC launch profile.",
      "display_name": "ONT SNV + Alignstats Kitchen Sink",
      "dryrun_dy_command": "bin/day_run produce_alignstats produce_sentdont_snv_vcf produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 5 -k -n",
      "dy_command": "bin/day_run produce_alignstats produce_sentdont_snv_vcf produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 5 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [
          [
            "ONT_R1_FQ",
            "ONT_R2_FQ"
          ],
          [
            "ONT_FASTQ_PREFIX"
          ],
          [
            "ONT_CRAM",
            "ONT_CRAM_ALIGNER",
            "ONT_CRAM_SNV_CALLER"
          ],
          [
            "ONT_BAM",
            "ONT_BAM_ALIGNER",
            "ONT_BAM_SNV_CALLER"
          ]
        ],
        "required_run_context_values": {},
        "required_source_columns": []
      },
      "jobs": 5,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "sentdont"
      ],
      "sv_callers": [],
      "targets": [
        "produce_alignstats",
        "produce_sentdont_snv_vcf",
        "produce_snv_concordances",
        "produce_relatedness",
        "produce_vep",
        "produce_multiqc_all"
      ],
      "validation_runs": []
    },
    {
      "aligners": [
        "sentmm2"
      ],
      "artifact_registration": null,
      "command_class": "sample_analysis",
      "command_id": "pacbio_snv_alignstats",
      "compatible_data_modes": [
        "pacbio_solo"
      ],
      "compatible_platforms": [
        "PACBIO"
      ],
      "datasource": "PacBio",
      "dedupers": [
        "na"
      ],
      "description": "PacBio HiFi Sentieon DeepVariant and alignment-statistics launch profile.",
      "display_name": "PacBio SNV + Alignstats",
      "dryrun_dy_command": "bin/day_run produce_sentmm2_align produce_na_dedup_cram produce_sentdpb_snv_vcf produce_alignstats produce_snv_concordances -p -j 2 -k -T 1 -n",
      "dy_command": "bin/day_run produce_sentmm2_align produce_na_dedup_cram produce_sentdpb_snv_vcf produce_alignstats produce_snv_concordances -p -j 2 -k -T 1",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [
          [
            "PACBIO_R1_FQ",
            "PACBIO_R2_FQ"
          ],
          [
            "PB_BAM",
            "PB_BAM_ALIGNER",
            "PB_BAM_SNV_CALLER"
          ]
        ],
        "required_run_context_values": {},
        "required_source_columns": []
      },
      "jobs": 2,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "sentdpb"
      ],
      "sv_callers": [],
      "targets": [
        "produce_sentmm2_align",
        "produce_na_dedup_cram",
        "produce_sentdpb_snv_vcf",
        "produce_alignstats",
        "produce_snv_concordances"
      ],
      "validation_runs": [
        {
          "cluster": "tstVer4-1-1b",
          "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
          "dayec_tag": "4.1.3",
          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
          "dayoa_tag": "1.0.21",
          "dryrun_analysis_id": "tvb_pacbio_snv_alignstats_5x_1021_dryrun",
          "dryrun_status": "success",
          "failure_cause": "",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "tvb_pacbio_snv_alignstats_5x_1021",
          "live_status": "success",
          "notes": "Live run completed with CRAM, VCF, alignstats, and concordance outputs.",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T073306Z",
          "status": "success",
          "tested_command": "bin/day_run produce_sentmm2_align produce_na_dedup_cram produce_sentdpb_snv_vcf produce_alignstats produce_snv_concordances -p -j 2 -k -T 1"
        }
      ]
    },
    {
      "aligners": [
        "roche"
      ],
      "artifact_registration": null,
      "command_class": "sample_analysis",
      "command_id": "roche_snv_alignstats",
      "compatible_data_modes": [
        "roche_solo"
      ],
      "compatible_platforms": [
        "ROCHE"
      ],
      "datasource": "Roche",
      "dedupers": [
        "na"
      ],
      "description": "Roche aligned BAM HaplotypeCaller and alignment-statistics launch profile.",
      "display_name": "Roche SNV + Alignstats",
      "dryrun_dy_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_rochehc_snv_vcf -p -j 5 -k -n",
      "dy_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_rochehc_snv_vcf -p -j 5 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {},
        "required_source_columns": [
          "ROCHE_BAM",
          "ROCHE_BAM_ALIGNER",
          "ROCHE_BAM_SNV_CALLER"
        ]
      },
      "jobs": 5,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "rochehc"
      ],
      "sv_callers": [],
      "targets": [
        "produce_alignstats",
        "produce_na_dedup_cram",
        "produce_rochehc_snv_vcf"
      ],
      "validation_runs": [
        {
          "cluster": "tstVer4-1-1b",
          "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
          "dayec_tag": "4.1.3",
          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
          "dayoa_tag": "1.0.21",
          "dryrun_analysis_id": "tvb_roche_snv_alignstats_5x_1021_dryrun",
          "dryrun_status": "failed",
          "failure_cause": "Dry-run failed while preparing Roche/GATK containers: missing Singularity image /fsx/resources/environments/containers/ubuntu/ip-10-0-0-103/7a424a40c6fd659f4d052893dd3554fa.simg.",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "",
          "live_status": "not_run",
          "notes": "",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T073504Z",
          "status": "failed",
          "tested_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_rochehc_snv_vcf -p -j 5 -k"
        }
      ]
    },
    {
      "aligners": [
        "sent"
      ],
      "artifact_registration": null,
      "command_class": "sample_analysis",
      "command_id": "hybrid_ilmn_ont_snv",
      "compatible_data_modes": [
        "hybrid_ilmn_ont"
      ],
      "compatible_platforms": [
        "ILMN",
        "ONT"
      ],
      "datasource": "Hybrid ILMN+ONT",
      "dedupers": [
        "dmd"
      ],
      "description": "Hybrid Illumina plus ONT refactored Sentieon HIOMR SNV/SV launch profile.",
      "display_name": "Hybrid ILMN+ONT HIOMR SNV/SV",
      "dryrun_dy_command": "bin/day_run produce_snv_concordances produce_sentdhiomr_sv produce_sentdhiomr_snv_vcf --config 'dedupers=[\"dmd\"]' -p -j 100 -k -n",
      "dy_command": "bin/day_run produce_snv_concordances produce_sentdhiomr_sv produce_sentdhiomr_snv_vcf --config 'dedupers=[\"dmd\"]' -p -j 100 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {},
        "required_source_columns": [
          "ILMN_R1_FQ",
          "ILMN_R2_FQ",
          "ONT_CRAM",
          "ONT_CRAM_ALIGNER",
          "ONT_CRAM_SNV_CALLER"
        ]
      },
      "jobs": 100,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "sentdhiomr"
      ],
      "sv_callers": [
        "sentdhiomr"
      ],
      "targets": [
        "produce_snv_concordances",
        "produce_sentdhiomr_sv",
        "produce_sentdhiomr_snv_vcf"
      ],
      "validation_runs": [
        {
          "cluster": "tstVer4-1-1b",
          "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
          "dayec_tag": "4.1.3",
          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
          "dayoa_tag": "1.0.21",
          "dryrun_analysis_id": "tvb_hybrid_ilmn_ont_snv_5x5x_1021_dryrun",
          "dryrun_status": "success",
          "failure_cause": "",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "tvb_hybrid_ilmn_ont_snv_5x5x_1021",
          "live_status": "success",
          "notes": "Live run completed with sentdhiomr SNV/SV and concordance outputs.",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T074001Z",
          "status": "success",
          "tested_command": "bin/day_run produce_snv_concordances produce_sentdhiomr_sv produce_sentdhiomr_snv_vcf --config 'dedupers=[\"dmd\"]' -p -j 100 -k"
        }
      ]
    },
    {
      "aligners": [
        "sent"
      ],
      "artifact_registration": {
        "enabled": true,
        "evidence_manifest_path": "results/day/{genome}/reports/dayoa_evidence_manifest.json",
        "identity": {
          "analysis_euid": "{analysis_id}",
          "assay_id": "",
          "project_euid": "",
          "run_euid": "{analysis_id}",
          "workset_euid": ""
        },
        "include_classifications": [
          "multiqc_html",
          "multiqc_data_json",
          "multiqc_general_stats",
          "multiqc_sources",
          "multiqc_log",
          "custom_mqc_tsv",
          "staging_manifest",
          "benchmark"
        ],
        "include_paths": [
          "results/day/{genome}/reports/DAY_final_multiqc.html",
          "results/day/{genome}/reports/DAY_final_multiqc_data/**",
          "results/day/{genome}/reports/multiqc_inputs/final/manifest.tsv",
          "results/day/{genome}/other_reports/*_mqc.tsv"
        ],
        "multiqc_report_kind": "final",
        "multiqc_version": "1.35",
        "parser_family_hint": "multiqc",
        "require_existing": true
      },
      "command_class": "sample_analysis",
      "command_id": "hybrid_ilmn_ont_snv_kitchensink",
      "compatible_data_modes": [
        "hybrid_ilmn_ont"
      ],
      "compatible_platforms": [
        "ILMN",
        "ONT"
      ],
      "datasource": "Hybrid ILMN+ONT",
      "dedupers": [
        "dmd"
      ],
      "description": "Hybrid Illumina plus ONT refactored Sentieon HIOMR SNV/SV, relatedness, VEP annotation, and final MultiQC launch profile.",
      "display_name": "Hybrid ILMN+ONT HIOMR SNV/SV Kitchen Sink",
      "dryrun_dy_command": "bin/day_run produce_snv_concordances produce_sentdhiomr_sv produce_sentdhiomr_snv_vcf produce_relatedness produce_vep produce_multiqc_all --config 'dedupers=[\"dmd\"]' 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k -n",
      "dy_command": "bin/day_run produce_snv_concordances produce_sentdhiomr_sv produce_sentdhiomr_snv_vcf produce_relatedness produce_vep produce_multiqc_all --config 'dedupers=[\"dmd\"]' 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {},
        "required_source_columns": [
          "ILMN_R1_FQ",
          "ILMN_R2_FQ",
          "ONT_CRAM",
          "ONT_CRAM_ALIGNER",
          "ONT_CRAM_SNV_CALLER"
        ]
      },
      "jobs": 100,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "sentdhiomr"
      ],
      "sv_callers": [
        "sentdhiomr"
      ],
      "targets": [
        "produce_snv_concordances",
        "produce_sentdhiomr_sv",
        "produce_sentdhiomr_snv_vcf",
        "produce_relatedness",
        "produce_vep",
        "produce_multiqc_all"
      ],
      "validation_runs": []
    },
    {
      "aligners": [
        "sent"
      ],
      "artifact_registration": null,
      "command_class": "sample_analysis",
      "command_id": "inflection-bjuice-product-v0.1",
      "compatible_data_modes": [
        "hybrid_ilmn_ont"
      ],
      "compatible_platforms": [
        "ILMN",
        "ONT"
      ],
      "datasource": "Hybrid ILMN+ONT",
      "dedupers": [
        "dmd"
      ],
      "description": "Inflection hybrid Illumina plus ONT HIOMR product profile with align, dmd CRAM, SNV, SV, CNV, mito, segdup limited to CYP11B1/NCF1/SMN1, expansionhunter, and concordance targets.",
      "display_name": "Inflection BJuice Product v0.1",
      "dryrun_dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentdhiomr_sv produce_snv_concordances produce_sentdhiomr_snv_vcf produce_sentdhiomr_cnv produce_sentdhiomr_mito produce_sentdhiomr_segdup produce_expansionhunter --config 'sentdhiomr={\"segdup_genes\":\"CYP11B1,NCF1,SMN1\"}' -j 125 -p -k -n",
      "dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentdhiomr_sv produce_snv_concordances produce_sentdhiomr_snv_vcf produce_sentdhiomr_cnv produce_sentdhiomr_mito produce_sentdhiomr_segdup produce_expansionhunter --config 'sentdhiomr={\"segdup_genes\":\"CYP11B1,NCF1,SMN1\"}' -j 125 -p -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {},
        "required_source_columns": [
          "ILMN_R1_FQ",
          "ILMN_R2_FQ",
          "ONT_CRAM",
          "ONT_CRAM_ALIGNER",
          "ONT_CRAM_SNV_CALLER"
        ]
      },
      "jobs": 125,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "sentdhiomr"
      ],
      "sv_callers": [
        "sentdhiomr"
      ],
      "targets": [
        "produce_sent_align",
        "produce_dmd_dedup_cram",
        "produce_sentdhiomr_sv",
        "produce_snv_concordances",
        "produce_sentdhiomr_snv_vcf",
        "produce_sentdhiomr_cnv",
        "produce_sentdhiomr_mito",
        "produce_sentdhiomr_segdup",
        "produce_expansionhunter"
      ],
      "validation_runs": []
    },
    {
      "aligners": [
        "ug"
      ],
      "artifact_registration": null,
      "command_class": "sample_analysis",
      "command_id": "hybrid_ultima_ont_snv",
      "compatible_data_modes": [
        "hybrid_ug_ont"
      ],
      "compatible_platforms": [
        "ULTIMA",
        "ONT"
      ],
      "datasource": "Hybrid Ultima+ONT",
      "dedupers": [
        "na"
      ],
      "description": "Hybrid Ultima plus ONT refactored modular Sentieon HUOMR SNV launch profile.",
      "display_name": "Hybrid Ultima+ONT HUOMR SNV",
      "dryrun_dy_command": "bin/day_run produce_sentdhuomr_snv_vcf produce_alignstats produce_snv_concordances -p -j 100 -k -n",
      "dy_command": "bin/day_run produce_sentdhuomr_snv_vcf produce_alignstats produce_snv_concordances -p -j 100 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {},
        "required_source_columns": [
          "ULTIMA_CRAM",
          "ULTIMA_CRAM_ALIGNER",
          "ULTIMA_CRAM_SNV_CALLER",
          "ONT_CRAM",
          "ONT_CRAM_ALIGNER",
          "ONT_CRAM_SNV_CALLER"
        ]
      },
      "jobs": 100,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "sentdhuomr"
      ],
      "sv_callers": [],
      "targets": [
        "produce_sentdhuomr_snv_vcf",
        "produce_alignstats",
        "produce_snv_concordances"
      ],
      "validation_runs": [
        {
          "cluster": "tstVer4-1-1b",
          "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
          "dayec_tag": "4.1.3",
          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
          "dayoa_tag": "1.0.21",
          "dryrun_analysis_id": "tvb_hybrid_ultima_ont_snv_5x5x_1021_dryrun",
          "dryrun_status": "success",
          "failure_cause": "Live run failed in sentdhuomr_hybrid_select: ModuleNotFoundError: No module named 'sentieon_cli' while resolving files('sentieon_cli.scripts').joinpath('hybrid_select.py').",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "tvb_hybrid_ultima_ont_snv_5x5x_1021",
          "live_status": "failed",
          "notes": "Dry-run passed; live failure was new after the r-suffix command and pass-through staging avoided the prior basename collision.",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T074404Z",
          "status": "failed",
          "tested_command": "bin/day_run produce_sentdhuomr_snv_vcf produce_alignstats produce_snv_concordances -p -j 100 -k"
        }
      ]
    },
    {
      "aligners": [
        "sentcg"
      ],
      "artifact_registration": null,
      "command_class": "sample_analysis",
      "command_id": "complete_genomics_mgi_snv_concordance",
      "compatible_data_modes": [
        "complete_genomics_solo"
      ],
      "compatible_platforms": [
        "CG/MGI"
      ],
      "datasource": "Complete Genomics/MGI",
      "dedupers": [
        "dmd"
      ],
      "description": "Complete Genomics/MGI Sentieon sentcg/dmd/cgt7p launch profile.",
      "display_name": "Complete Genomics/MGI SNV + Concordance",
      "dryrun_dy_command": "bin/day_run produce_sentcg_align produce_dmd_dedup_cram produce_cgt7p_snv_vcf produce_alignstats produce_snv_concordances -p -j 20 -k -T 1 --retries 0 --rerun-incomplete --keep-incomplete -n",
      "dy_command": "bin/day_run produce_sentcg_align produce_dmd_dedup_cram produce_cgt7p_snv_vcf produce_alignstats produce_snv_concordances -p -j 20 -k -T 1 --retries 0 --rerun-incomplete --keep-incomplete",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "sample_manifest",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {},
        "required_source_columns": [
          "CG_R1_FQ",
          "CG_R2_FQ"
        ]
      },
      "jobs": 20,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": false,
      "requires_staging": true,
      "runtime_parameters": {},
      "snv_callers": [
        "cgt7p"
      ],
      "sv_callers": [],
      "targets": [
        "produce_sentcg_align",
        "produce_dmd_dedup_cram",
        "produce_cgt7p_snv_vcf",
        "produce_alignstats",
        "produce_snv_concordances"
      ],
      "validation_runs": [
        {
          "cluster": "tstVer4-1-1b",
          "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
          "dayec_tag": "4.1.3",
          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
          "dayoa_tag": "1.0.21",
          "dryrun_analysis_id": "",
          "dryrun_status": "blocked",
          "failure_cause": "Blocked before dry-run because the candidate mate pair was not verified: _386_1 was 90,600,002,744 bytes, _386_2 was 10,794,018,984 bytes, and nearby _388_2 was 97,844,317,264 bytes.",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "",
          "live_status": "blocked",
          "notes": "",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "docs/plans/20260525T063158Z_tstver411b_inputs/complete_genomics_mgi_hg003_candidate_blocked.tsv",
          "status": "blocked",
          "tested_command": "bin/day_run produce_sentcg_align produce_dmd_dedup_cram produce_cgt7p_snv_vcf produce_alignstats produce_snv_concordances -p -j 20 -k -T 1 --retries 0 --rerun-incomplete --keep-incomplete"
        }
      ]
    },
    {
      "aligners": [],
      "artifact_registration": null,
      "command_class": "run_analysis",
      "command_id": "illumina_run_qc",
      "compatible_data_modes": [
        "run_directory_mount"
      ],
      "compatible_platforms": [
        "ILMN"
      ],
      "datasource": "Illumina",
      "dedupers": [],
      "description": "Illumina run-folder QC from a mounted or explicit S3 run context.",
      "display_name": "Illumina Run QC",
      "dryrun_dy_command": "bin/day_run produce_illumina_run_qc -p -j 5 -k -n",
      "dy_command": "bin/day_run produce_illumina_run_qc -p -j 5 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "run_context",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {
          "PLATFORM": "ILMN"
        },
        "required_source_columns": []
      },
      "jobs": 5,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": true,
      "requires_staging": false,
      "runtime_parameters": {
        "run_context_file": "config/runs.tsv",
        "samples_table": ".test_data/data/samples.tsv",
        "units_table": ".test_data/data/units.tsv"
      },
      "snv_callers": [],
      "sv_callers": [],
      "targets": [
        "produce_illumina_run_qc"
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      "validation_runs": [
        {
          "cluster": "tstVer4-1-1b",
          "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
          "dayec_tag": "4.1.3",
          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
          "dayoa_tag": "1.0.21",
          "dryrun_analysis_id": "tvb_illumina_run_qc_1021_dryrun",
          "dryrun_status": "failed",
          "failure_cause": "Dry-run failed: WorkflowError reported config/units.tsv was not found and requested config/units.tsv or --config units_table=/path/to/units.tsv.",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "",
          "live_status": "not_run",
          "notes": "",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "/fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/",
          "status": "failed",
          "tested_command": "bin/day_run produce_illumina_run_qc -p -j 5 -k --config run_context_file=config/runs.tsv samples_table=.test_data/data/samples.tsv units_table=.test_data/data/units.tsv"
        }
      ]
    },
    {
      "aligners": [],
      "artifact_registration": null,
      "command_class": "run_analysis",
      "command_id": "illumina_bclconvert",
      "compatible_data_modes": [
        "run_directory_mount"
      ],
      "compatible_platforms": [
        "ILMN"
      ],
      "datasource": "Illumina",
      "dedupers": [],
      "description": "Illumina demultiplexing through the pinned nf-core/bclconvert 4.0.3 container from a mounted run directory, with generated units table, demux metric TSVs, and focused BCL Convert MultiQC. This command does not run FastQC.",
      "display_name": "Illumina nf-core BCL Convert",
      "dryrun_dy_command": "bin/day_run produce_bclconvert_fastqs_and_metrics -p -j 20 -k -n",
      "dy_command": "bin/day_run produce_bclconvert_fastqs_and_metrics -p -j 20 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "run_context",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {
          "PLATFORM": "ILMN"
        },
        "required_source_columns": []
      },
      "jobs": 20,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": true,
      "requires_staging": false,
      "runtime_parameters": {
        "run_context_file": "config/runs.tsv",
        "samples_table": ".test_data/data/bclconvert/samples.tsv",
        "units_table": ".test_data/data/bclconvert/units.tsv"
      },
      "snv_callers": [],
      "sv_callers": [],
      "targets": [
        "produce_bclconvert_fastqs_and_metrics"
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      "validation_runs": [
        {
          "cluster": "tstVer4-1-1b",
          "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
          "dayec_tag": "4.1.3",
          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
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          "dryrun_analysis_id": "tvb_illumina_bclconvert_1021_dryrun",
          "dryrun_status": "failed",
          "failure_cause": "Dry-run failed: WorkflowError reported no read pairs specified for analysis unit 20260514_LH01106_0009_B23TVLGLT4.",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "",
          "live_status": "not_run",
          "notes": "",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "/fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/",
          "status": "failed",
          "tested_command": "bin/day_run produce_bclconvert_fastqs_and_metrics -p -j 20 -k --config run_context_file=config/runs.tsv samples_table=.test_data/data/bclconvert/samples.tsv units_table=.test_data/data/bclconvert/units.tsv"
        }
      ]
    },
    {
      "aligners": [],
      "artifact_registration": null,
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      "datasource": "Illumina",
      "dedupers": [],
      "description": "Mounted Illumina run-folder QC plus demultiplexing through the pinned nf-core/bclconvert 4.0.3 container, generated units, demux metric TSVs, and focused BCL Convert MultiQC in one run-analysis output tree. This command does not run FastQC.",
      "display_name": "Illumina Run QC + nf-core BCL Convert",
      "dryrun_dy_command": "bin/day_run produce_illumina_run_qc_and_bclconvert -p -j 20 -k -n",
      "dy_command": "bin/day_run produce_illumina_run_qc_and_bclconvert -p -j 20 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "run_context",
      "input_requirements": {
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        "required_run_context_values": {
          "PLATFORM": "ILMN"
        },
        "required_source_columns": []
      },
      "jobs": 20,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
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      "requires_run_mount": true,
      "requires_staging": false,
      "runtime_parameters": {
        "run_context_file": "config/runs.tsv",
        "samples_table": ".test_data/data/bclconvert/samples.tsv",
        "units_table": ".test_data/data/bclconvert/units.tsv"
      },
      "snv_callers": [],
      "sv_callers": [],
      "targets": [
        "produce_illumina_run_qc_and_bclconvert"
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      "validation_runs": []
    },
    {
      "aligners": [],
      "artifact_registration": null,
      "command_class": "run_analysis",
      "command_id": "ont_run_qc",
      "compatible_data_modes": [
        "run_directory_mount"
      ],
      "compatible_platforms": [
        "ONT"
      ],
      "datasource": "ONT",
      "dedupers": [],
      "description": "ONT mounted run-folder QC plus demux FASTQ SeqKit/Nanoq/NanoStat/NanoPlot outputs and focused demux MultiQC in one run-analysis output tree.",
      "display_name": "ONT Run QC + Demux MultiQC",
      "dryrun_dy_command": "bin/day_run produce_ont_run_qc_and_demux_multiqc -p -j 5 -k -n",
      "dy_command": "bin/day_run produce_ont_run_qc_and_demux_multiqc -p -j 5 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "run_context",
      "input_requirements": {
        "accepted_source_column_sets": [],
        "required_run_context_values": {
          "PLATFORM": "ONT"
        },
        "required_source_columns": []
      },
      "jobs": 5,
      "launcher": "workflow_launch",
      "no_containerized": false,
      "optional_features": {},
      "repository": "daylily-omics-analysis",
      "requires_run_mount": true,
      "requires_staging": false,
      "runtime_parameters": {
        "run_context_file": "config/runs.tsv",
        "samples_table": ".test_data/data/samples.tsv",
        "units_table": ".test_data/data/units.tsv"
      },
      "snv_callers": [],
      "sv_callers": [],
      "targets": [
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      "validation_runs": [
        {
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          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
          "dayoa_tag": "1.0.21",
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          "dryrun_status": "failed",
          "failure_cause": "Dry-run failed: WorkflowError reported config/units.tsv was not found and requested config/units.tsv or --config units_table=/path/to/units.tsv.",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "",
          "live_status": "not_run",
          "notes": "",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "/fsx/run_dir_mounts/20260513_ONT_HG003/",
          "status": "failed",
          "tested_command": "bin/day_run produce_ont_run_qc -p -j 5 -k --config run_context_file=config/runs.tsv samples_table=.test_data/data/samples.tsv units_table=.test_data/data/units.tsv"
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      ]
    },
    {
      "aligners": [],
      "artifact_registration": null,
      "command_class": "run_analysis",
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      "compatible_data_modes": [
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      "compatible_platforms": [
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      "datasource": "Ultima",
      "dedupers": [],
      "description": "Ultima run-folder QC from a mounted run context.",
      "display_name": "Ultima Run QC",
      "dryrun_dy_command": "bin/day_run produce_ultima_run_qc -p -j 5 -k -n",
      "dy_command": "bin/day_run produce_ultima_run_qc -p -j 5 -k",
      "genome": "hg38_broad",
      "git_tag": "2.0.23",
      "input_contract": "run_context",
      "input_requirements": {
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        "required_run_context_values": {
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        "required_source_columns": []
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      "jobs": 5,
      "launcher": "workflow_launch",
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      "optional_features": {},
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      "requires_run_mount": true,
      "requires_staging": false,
      "runtime_parameters": {
        "run_context_file": "config/runs.tsv",
        "samples_table": ".test_data/data/samples.tsv",
        "units_table": ".test_data/data/units.tsv"
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      "snv_callers": [],
      "sv_callers": [],
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      "validation_runs": [
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          "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
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          "failure_cause": "Dry-run failed: WorkflowError reported config/units.tsv was not found and requested config/units.tsv or --config units_table=/path/to/units.tsv.",
          "generated_at": "2026-05-25T20:04:39Z",
          "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
          "live_analysis_id": "",
          "live_status": "not_run",
          "notes": "",
          "region": "us-west-2",
          "region_az": "us-west-2d",
          "report_path": "docs/tstver411b_command_catalog_test_results.md",
          "run_id": "tstver411b_dayoa_catalog_recipe_validation",
          "stage_or_context": "/fsx/run_dir_mounts/602221-20260417_2346/",
          "status": "failed",
          "tested_command": "bin/day_run produce_ultima_run_qc -p -j 5 -k --config run_context_file=config/runs.tsv samples_table=.test_data/data/samples.tsv units_table=.test_data/data/units.tsv"
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  ],
  "default_repository": "daylily-omics-analysis",
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      "source_table": {
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        "required_columns": [
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          "PLATFORM",
          "RUN_DIR",
          "SOURCE_S3_URI",
          "MOUNT_ID",
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          "BASECALLING_STATE",
          "RUN_STATUS",
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          "REGION",
          "PROFILE"
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      }
    },
    "sample_manifest": {
      "description": "DayEC stages analysis_samples.tsv into DayOA config/samples.tsv and config/units.tsv.",
      "generated_tables": {
        "samples_tsv": {
          "path": "config/samples.tsv",
          "required_columns": [
            "SAMPLEID",
            "SAMPLESOURCE",
            "SAMPLECLASS",
            "BIOLOGICAL_SEX",
            "CONCORDANCE_CONTROL_PATH",
            "IS_POSITIVE_CONTROL",
            "IS_NEGATIVE_CONTROL",
            "SAMPLE_TYPE",
            "TUM_NRM_SAMPLEID_MATCH",
            "EXTERNAL_SAMPLE_ID",
            "N_X",
            "N_Y",
            "TRUTH_DATA_DIR"
          ]
        },
        "units_tsv": {
          "path": "config/units.tsv",
          "required_columns": [
            "RUNID",
            "SAMPLEID",
            "EXPERIMENTID",
            "LANEID",
            "BARCODEID",
            "LIBPREP",
            "SEQ_VENDOR",
            "SEQ_PLATFORM",
            "ILMN_R1_PATH",
            "ILMN_R2_PATH",
            "PACBIO_R1_PATH",
            "PACBIO_R2_PATH",
            "ONT_R1_PATH",
            "ONT_R2_PATH",
            "UG_R1_PATH",
            "UG_R2_PATH",
            "SUBSAMPLE_PCT",
            "ILMN_TRIM_READ_LENGTH",
            "SAMPLEUSE",
            "BWA_KMER",
            "DEEP_MODEL",
            "ULTIMA_CRAM",
            "ULTIMA_CRAM_ALIGNER",
            "ULTIMA_CRAM_SNV_CALLER",
            "ONT_CRAM",
            "ONT_CRAM_ALIGNER",
            "ONT_CRAM_SNV_CALLER",
            "PB_BAM",
            "PB_BAM_ALIGNER",
            "PB_BAM_SNV_CALLER",
            "ROCHE_BAM",
            "ROCHE_BAM_ALIGNER",
            "ROCHE_BAM_SNV_CALLER",
            "ROCHE_DOWNSAMPLE_RATIO",
            "LONGREADTRIM_READ_LENGTH",
            "LONGREADTRIM_MODE",
            "ULTIMA_SUBSAMPLE_PCT",
            "ONT_SUBSAMPLE_PCT",
            "ONT_BAM",
            "ONT_BAM_ALIGNER",
            "ONT_BAM_SNV_CALLER"
          ]
        }
      },
      "source_table": {
        "path": "analysis_samples.tsv",
        "required_columns": [
          "RUN_ID",
          "SAMPLE_ID",
          "EXPERIMENTID",
          "SAMPLE_TYPE",
          "LIB_PREP",
          "SEQ_VENDOR",
          "SEQ_PLATFORM",
          "LANE",
          "SEQBC_ID"
        ]
      }
    }
  },
  "repositories": {
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      "analysis_commands": [
        {
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          "artifact_registration": null,
          "command_class": "utility",
          "command_id": "simple-test",
          "compatible_data_modes": [
            "none"
          ],
          "compatible_platforms": [
            "local"
          ],
          "datasource": "DayOA",
          "dedupers": [],
          "description": "Smoke-test DayOA shell initialization and local help target without staged sample inputs.",
          "display_name": "Simple Test",
          "dryrun_dy_command": "source dyoainit; dy-a local hg38; dy-r -p -k -j 1 help",
          "dy_command": "source dyoainit; dy-a local hg38; dy-r -p -k -j 1 help",
          "genome": "hg38",
          "git_tag": "2.0.23",
          "input_contract": "none",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {},
            "required_source_columns": []
          },
          "jobs": 1,
          "launcher": "workflow_launch",
          "no_containerized": true,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": false,
          "runtime_parameters": {},
          "snv_callers": [],
          "sv_callers": [],
          "targets": [
            "help"
          ],
          "validation_runs": []
        },
        {
          "aligners": [
            "sent"
          ],
          "artifact_registration": null,
          "command_class": "sample_analysis",
          "command_id": "illumina_snv_alignstats",
          "compatible_data_modes": [
            "ilmn_solo"
          ],
          "compatible_platforms": [
            "ILMN"
          ],
          "datasource": "Illumina",
          "dedupers": [
            "dmd"
          ],
          "description": "Illumina WGS Sentieon DNAscope and alignment-statistics launch profile.",
          "display_name": "Illumina SNV + Alignstats",
          "dryrun_dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_snv_concordances produce_alignstats -p -k -j 20 -n",
          "dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_snv_concordances produce_alignstats -p -k -j 20",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {},
            "required_source_columns": [
              "ILMN_R1_FQ",
              "ILMN_R2_FQ"
            ]
          },
          "jobs": 20,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "sentd"
          ],
          "sv_callers": [],
          "targets": [
            "produce_sent_align",
            "produce_dmd_dedup_cram",
            "produce_sentd_snv_vcf",
            "produce_snv_concordances",
            "produce_alignstats"
          ],
          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "tvb_illumina_snv_alignstats_5x_1021_dryrun",
              "dryrun_status": "success",
              "failure_cause": "",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "tvb_illumina_snv_alignstats_5x_1021",
              "live_status": "success",
              "notes": "Live run completed with CRAM, VCF, alignstats, and concordance outputs.",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T071517Z",
              "status": "success",
              "tested_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_snv_concordances produce_alignstats -p -k -j 20"
            }
          ]
        },
        {
          "aligners": [
            "sent"
          ],
          "artifact_registration": {
            "enabled": true,
            "evidence_manifest_path": "results/day/{genome}/reports/dayoa_evidence_manifest.json",
            "identity": {
              "analysis_euid": "{analysis_id}",
              "assay_id": "",
              "project_euid": "",
              "run_euid": "{analysis_id}",
              "workset_euid": ""
            },
            "include_classifications": [
              "multiqc_html",
              "multiqc_data_json",
              "multiqc_general_stats",
              "multiqc_sources",
              "multiqc_log",
              "custom_mqc_tsv",
              "staging_manifest",
              "benchmark"
            ],
            "include_paths": [
              "results/day/{genome}/reports/DAY_final_multiqc.html",
              "results/day/{genome}/reports/DAY_final_multiqc_data/**",
              "results/day/{genome}/reports/multiqc_inputs/final/manifest.tsv",
              "results/day/{genome}/other_reports/*_mqc.tsv"
            ],
            "multiqc_report_kind": "final",
            "multiqc_version": "1.35",
            "parser_family_hint": "multiqc",
            "require_existing": true
          },
          "command_class": "sample_analysis",
          "command_id": "illumina_snv_alignstats_relatedness_vep_multiqc",
          "compatible_data_modes": [
            "ilmn_solo"
          ],
          "compatible_platforms": [
            "ILMN"
          ],
          "datasource": "Illumina",
          "dedupers": [
            "dmd"
          ],
          "description": "Illumina WGS Sentieon DNAscope, alignment statistics, relatedness, VEP annotation, and final MultiQC launch profile.",
          "display_name": "Illumina SNV + Alignstats + Relatedness + VEP MultiQC",
          "dryrun_dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k -n",
          "dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {},
            "required_source_columns": [
              "ILMN_R1_FQ",
              "ILMN_R2_FQ"
            ]
          },
          "jobs": 100,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "sentd"
          ],
          "sv_callers": [],
          "targets": [
            "produce_sent_align",
            "produce_dmd_dedup_cram",
            "produce_sentd_snv_vcf",
            "produce_alignstats",
            "produce_snv_concordances",
            "produce_relatedness",
            "produce_vep",
            "produce_multiqc_all"
          ],
          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "tvb_illumina_related_vep_multiqc_5x_1021_dryrun",
              "dryrun_status": "success",
              "failure_cause": "",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "tvb_illumina_related_vep_multiqc_5x_1021",
              "live_status": "success",
              "notes": "Live run completed with CRAM, VCF, alignstats, concordance, MultiQC, and relatedness outputs.",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T072540Z",
              "status": "success",
              "tested_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k"
            }
          ]
        },
        {
          "aligners": [
            "sent"
          ],
          "artifact_registration": {
            "enabled": true,
            "evidence_manifest_path": "results/day/{genome}/reports/dayoa_evidence_manifest.json",
            "identity": {
              "analysis_euid": "{analysis_id}",
              "assay_id": "",
              "project_euid": "",
              "run_euid": "{analysis_id}",
              "workset_euid": ""
            },
            "include_classifications": [
              "multiqc_html",
              "multiqc_data_json",
              "multiqc_general_stats",
              "multiqc_sources",
              "multiqc_log",
              "custom_mqc_tsv",
              "staging_manifest",
              "benchmark"
            ],
            "include_paths": [
              "results/day/{genome}/reports/DAY_final_multiqc.html",
              "results/day/{genome}/reports/DAY_final_multiqc_data/**",
              "results/day/{genome}/reports/multiqc_inputs/final/manifest.tsv",
              "results/day/{genome}/other_reports/*_mqc.tsv"
            ],
            "multiqc_report_kind": "final",
            "multiqc_version": "1.35",
            "parser_family_hint": "multiqc",
            "require_existing": true
          },
          "command_class": "sample_analysis",
          "command_id": "illumina_hg002_kitchensink_multiqc",
          "compatible_data_modes": [
            "ilmn_solo"
          ],
          "compatible_platforms": [
            "ILMN"
          ],
          "datasource": "Illumina",
          "dedupers": [
            "dmd"
          ],
          "description": "HG002 Illumina WGS Sentieon DNAscope, dmd CRAM, concordance, relatedness, contamination identity, VEP, ExpansionHunter, HTD, metagenomics, and final MultiQC validation profile.",
          "display_name": "Illumina HG002 Kitchen Sink MultiQC",
          "dryrun_dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_gatk_contam_estimate produce_site_mix_contam_estimate produce_global_contam_check produce_vep produce_expansionhunter produce_htd_calls produce_metagenomics produce_multiqc_all --config 'aligners=[\"sent\"]' 'dedupers=[\"dmd\"]' 'snv_callers=[\"sentd\"]' 'htd_callers=[\"cyrius\"]' 'multiqc_qc={\"enable_tools\":[\"vep\",\"metagenomics\",\"contam_identity\"]}' -j 200 -p -k --rerun-triggers mtime -n",
          "dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_gatk_contam_estimate produce_site_mix_contam_estimate produce_global_contam_check produce_vep produce_expansionhunter produce_htd_calls produce_metagenomics produce_multiqc_all --config 'aligners=[\"sent\"]' 'dedupers=[\"dmd\"]' 'snv_callers=[\"sentd\"]' 'htd_callers=[\"cyrius\"]' 'multiqc_qc={\"enable_tools\":[\"vep\",\"metagenomics\",\"contam_identity\"]}' -j 200 -p -k --rerun-triggers mtime",
          "genome": "hg38",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {},
            "required_source_columns": [
              "ILMN_R1_FQ",
              "ILMN_R2_FQ"
            ]
          },
          "jobs": 200,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "sentd"
          ],
          "sv_callers": [],
          "targets": [
            "produce_sent_align",
            "produce_dmd_dedup_cram",
            "produce_sentd_snv_vcf",
            "produce_alignstats",
            "produce_snv_concordances",
            "produce_relatedness",
            "produce_gatk_contam_estimate",
            "produce_site_mix_contam_estimate",
            "produce_global_contam_check",
            "produce_vep",
            "produce_expansionhunter",
            "produce_htd_calls",
            "produce_metagenomics",
            "produce_multiqc_all"
          ],
          "validation_runs": [
            {
              "cluster": "goodole3",
              "dayec_commit": "fbad3b802f2886afdc011d41228c12a1b9094322",
              "dayec_tag": "5.0.20-dev",
              "dayoa_commit": "b377b8b557306fbb6832763a39661ce36d6f4bbd",
              "dayoa_tag": "2.0.19",
              "dryrun_analysis_id": "dayoa_2017_hg002_kitchensink_j200_readhapsfix2_151101_dryrun",
              "dryrun_status": "success",
              "failure_cause": "",
              "generated_at": "2026-05-28T15:11:45Z",
              "ledger_path": "docs/plans/20260528T152607Z_dayoa_2017_release_train_ledger.md",
              "live_analysis_id": "dayoa_2017_hg002_kitchensink_j200_readhapsfix2_151101",
              "live_status": "success",
              "notes": "Headnode run used the dy-r alias with the same targets/config on the 2.0.17 clone plus local stabilization patches that were mirrored into DayOA release 2.0.19; final report was results/day/hg38/reports/DAY_final_multiqc.html.",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/plans/20260528T152607Z_dayoa_2017_release_train_ledger.md",
              "run_id": "dayoa_2017_hg002_kitchensink_j200_readhapsfix2_151101",
              "stage_or_context": "/fsx/analysis_results/ubuntu/2.0.17/daylily-omics-analysis",
              "status": "success",
              "tested_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentd_snv_vcf produce_alignstats produce_snv_concordances produce_relatedness produce_gatk_contam_estimate produce_site_mix_contam_estimate produce_global_contam_check produce_vep produce_expansionhunter produce_htd_calls produce_metagenomics produce_multiqc_all --config 'aligners=[\"sent\"]' 'dedupers=[\"dmd\"]' 'snv_callers=[\"sentd\"]' 'htd_callers=[\"cyrius\"]' 'multiqc_qc={\"enable_tools\":[\"vep\",\"metagenomics\",\"contam_identity\"]}' -j 200 -p -k --rerun-triggers mtime"
            }
          ]
        },
        {
          "aligners": [
            "ug"
          ],
          "artifact_registration": null,
          "command_class": "sample_analysis",
          "command_id": "ultima_snv_alignstats",
          "compatible_data_modes": [
            "ultima_solo"
          ],
          "compatible_platforms": [
            "ULTIMA"
          ],
          "datasource": "Ultima",
          "dedupers": [
            "na"
          ],
          "description": "Ultima CRAM/FASTQ Sentieon DNAscope and alignment-statistics launch profile.",
          "display_name": "Ultima SNV + Alignstats",
          "dryrun_dy_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_sentdug_snv_vcf produce_snv_concordances -p -j 20 -k -n",
          "dy_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_sentdug_snv_vcf produce_snv_concordances -p -j 20 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [
              [
                "UG_R1_FQ",
                "UG_R2_FQ"
              ],
              [
                "ULTIMA_CRAM",
                "ULTIMA_CRAM_ALIGNER",
                "ULTIMA_CRAM_SNV_CALLER"
              ]
            ],
            "required_run_context_values": {},
            "required_source_columns": []
          },
          "jobs": 20,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "sentdug"
          ],
          "sv_callers": [],
          "targets": [
            "produce_alignstats",
            "produce_na_dedup_cram",
            "produce_sentdug_snv_vcf",
            "produce_snv_concordances"
          ],
          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "tvb_ultima_snv_alignstats_5x_1021_dryrun",
              "dryrun_status": "success",
              "failure_cause": "",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "tvb_ultima_snv_alignstats_5x_1021",
              "live_status": "success",
              "notes": "Live run completed with VCF, alignstats, and concordance outputs.",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T072907Z",
              "status": "success",
              "tested_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_sentdug_snv_vcf produce_snv_concordances -p -j 20 -k"
            }
          ]
        },
        {
          "aligners": [
            "ug"
          ],
          "artifact_registration": {
            "enabled": true,
            "evidence_manifest_path": "results/day/{genome}/reports/dayoa_evidence_manifest.json",
            "identity": {
              "analysis_euid": "{analysis_id}",
              "assay_id": "",
              "project_euid": "",
              "run_euid": "{analysis_id}",
              "workset_euid": ""
            },
            "include_classifications": [
              "multiqc_html",
              "multiqc_data_json",
              "multiqc_general_stats",
              "multiqc_sources",
              "multiqc_log",
              "custom_mqc_tsv",
              "staging_manifest",
              "benchmark"
            ],
            "include_paths": [
              "results/day/{genome}/reports/DAY_final_multiqc.html",
              "results/day/{genome}/reports/DAY_final_multiqc_data/**",
              "results/day/{genome}/reports/multiqc_inputs/final/manifest.tsv",
              "results/day/{genome}/other_reports/*_mqc.tsv"
            ],
            "multiqc_report_kind": "final",
            "multiqc_version": "1.35",
            "parser_family_hint": "multiqc",
            "require_existing": true
          },
          "command_class": "sample_analysis",
          "command_id": "ultima_snv_alignstats_kitchensink",
          "compatible_data_modes": [
            "ultima_solo"
          ],
          "compatible_platforms": [
            "ULTIMA"
          ],
          "datasource": "Ultima",
          "dedupers": [
            "na"
          ],
          "description": "Ultima CRAM/FASTQ Sentieon DNAscope, alignment statistics, relatedness, VEP annotation, and final MultiQC launch profile.",
          "display_name": "Ultima SNV + Alignstats Kitchen Sink",
          "dryrun_dy_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_sentdug_snv_vcf produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k -n",
          "dy_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_sentdug_snv_vcf produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [
              [
                "UG_R1_FQ",
                "UG_R2_FQ"
              ],
              [
                "ULTIMA_CRAM",
                "ULTIMA_CRAM_ALIGNER",
                "ULTIMA_CRAM_SNV_CALLER"
              ]
            ],
            "required_run_context_values": {},
            "required_source_columns": []
          },
          "jobs": 100,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "sentdug"
          ],
          "sv_callers": [],
          "targets": [
            "produce_alignstats",
            "produce_na_dedup_cram",
            "produce_sentdug_snv_vcf",
            "produce_snv_concordances",
            "produce_relatedness",
            "produce_vep",
            "produce_multiqc_all"
          ],
          "validation_runs": []
        },
        {
          "aligners": [
            "ont"
          ],
          "artifact_registration": null,
          "command_class": "sample_analysis",
          "command_id": "ont_snv_alignstats",
          "compatible_data_modes": [
            "ont_solo"
          ],
          "compatible_platforms": [
            "ONT"
          ],
          "datasource": "ONT",
          "dedupers": [
            "na"
          ],
          "description": "ONT alignment, Sentieon DNAscope, and alignment-statistics launch profile.",
          "display_name": "ONT SNV + Alignstats",
          "dryrun_dy_command": "bin/day_run produce_alignstats produce_sentdont_snv_vcf produce_snv_concordances -p -j 5 -k -n",
          "dy_command": "bin/day_run produce_alignstats produce_sentdont_snv_vcf produce_snv_concordances -p -j 5 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [
              [
                "ONT_R1_FQ",
                "ONT_R2_FQ"
              ],
              [
                "ONT_FASTQ_PREFIX"
              ],
              [
                "ONT_CRAM",
                "ONT_CRAM_ALIGNER",
                "ONT_CRAM_SNV_CALLER"
              ],
              [
                "ONT_BAM",
                "ONT_BAM_ALIGNER",
                "ONT_BAM_SNV_CALLER"
              ]
            ],
            "required_run_context_values": {},
            "required_source_columns": []
          },
          "jobs": 5,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "sentdont"
          ],
          "sv_callers": [],
          "targets": [
            "produce_alignstats",
            "produce_sentdont_snv_vcf",
            "produce_snv_concordances"
          ],
          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "tvb_ont_snv_alignstats_5x_1021_dryrun",
              "dryrun_status": "success",
              "failure_cause": "",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "tvb_ont_snv_alignstats_5x_1021",
              "live_status": "success",
              "notes": "Live run completed with VCF, alignstats, and concordance outputs.",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T073112Z",
              "status": "success",
              "tested_command": "bin/day_run produce_alignstats produce_sentdont_snv_vcf produce_snv_concordances -p -j 5 -k"
            }
          ]
        },
        {
          "aligners": [
            "ont"
          ],
          "artifact_registration": {
            "enabled": true,
            "evidence_manifest_path": "results/day/{genome}/reports/dayoa_evidence_manifest.json",
            "identity": {
              "analysis_euid": "{analysis_id}",
              "assay_id": "",
              "project_euid": "",
              "run_euid": "{analysis_id}",
              "workset_euid": ""
            },
            "include_classifications": [
              "multiqc_html",
              "multiqc_data_json",
              "multiqc_general_stats",
              "multiqc_sources",
              "multiqc_log",
              "custom_mqc_tsv",
              "staging_manifest",
              "benchmark"
            ],
            "include_paths": [
              "results/day/{genome}/reports/DAY_final_multiqc.html",
              "results/day/{genome}/reports/DAY_final_multiqc_data/**",
              "results/day/{genome}/reports/multiqc_inputs/final/manifest.tsv",
              "results/day/{genome}/other_reports/*_mqc.tsv"
            ],
            "multiqc_report_kind": "final",
            "multiqc_version": "1.35",
            "parser_family_hint": "multiqc",
            "require_existing": true
          },
          "command_class": "sample_analysis",
          "command_id": "ont_snv_alignstats_kitchensink",
          "compatible_data_modes": [
            "ont_solo"
          ],
          "compatible_platforms": [
            "ONT"
          ],
          "datasource": "ONT",
          "dedupers": [
            "na"
          ],
          "description": "ONT alignment, Sentieon DNAscope, alignment statistics, relatedness, VEP annotation, and final MultiQC launch profile.",
          "display_name": "ONT SNV + Alignstats Kitchen Sink",
          "dryrun_dy_command": "bin/day_run produce_alignstats produce_sentdont_snv_vcf produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 5 -k -n",
          "dy_command": "bin/day_run produce_alignstats produce_sentdont_snv_vcf produce_snv_concordances produce_relatedness produce_vep produce_multiqc_all --config 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 5 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [
              [
                "ONT_R1_FQ",
                "ONT_R2_FQ"
              ],
              [
                "ONT_FASTQ_PREFIX"
              ],
              [
                "ONT_CRAM",
                "ONT_CRAM_ALIGNER",
                "ONT_CRAM_SNV_CALLER"
              ],
              [
                "ONT_BAM",
                "ONT_BAM_ALIGNER",
                "ONT_BAM_SNV_CALLER"
              ]
            ],
            "required_run_context_values": {},
            "required_source_columns": []
          },
          "jobs": 5,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "sentdont"
          ],
          "sv_callers": [],
          "targets": [
            "produce_alignstats",
            "produce_sentdont_snv_vcf",
            "produce_snv_concordances",
            "produce_relatedness",
            "produce_vep",
            "produce_multiqc_all"
          ],
          "validation_runs": []
        },
        {
          "aligners": [
            "sentmm2"
          ],
          "artifact_registration": null,
          "command_class": "sample_analysis",
          "command_id": "pacbio_snv_alignstats",
          "compatible_data_modes": [
            "pacbio_solo"
          ],
          "compatible_platforms": [
            "PACBIO"
          ],
          "datasource": "PacBio",
          "dedupers": [
            "na"
          ],
          "description": "PacBio HiFi Sentieon DeepVariant and alignment-statistics launch profile.",
          "display_name": "PacBio SNV + Alignstats",
          "dryrun_dy_command": "bin/day_run produce_sentmm2_align produce_na_dedup_cram produce_sentdpb_snv_vcf produce_alignstats produce_snv_concordances -p -j 2 -k -T 1 -n",
          "dy_command": "bin/day_run produce_sentmm2_align produce_na_dedup_cram produce_sentdpb_snv_vcf produce_alignstats produce_snv_concordances -p -j 2 -k -T 1",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [
              [
                "PACBIO_R1_FQ",
                "PACBIO_R2_FQ"
              ],
              [
                "PB_BAM",
                "PB_BAM_ALIGNER",
                "PB_BAM_SNV_CALLER"
              ]
            ],
            "required_run_context_values": {},
            "required_source_columns": []
          },
          "jobs": 2,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "sentdpb"
          ],
          "sv_callers": [],
          "targets": [
            "produce_sentmm2_align",
            "produce_na_dedup_cram",
            "produce_sentdpb_snv_vcf",
            "produce_alignstats",
            "produce_snv_concordances"
          ],
          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "tvb_pacbio_snv_alignstats_5x_1021_dryrun",
              "dryrun_status": "success",
              "failure_cause": "",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "tvb_pacbio_snv_alignstats_5x_1021",
              "live_status": "success",
              "notes": "Live run completed with CRAM, VCF, alignstats, and concordance outputs.",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T073306Z",
              "status": "success",
              "tested_command": "bin/day_run produce_sentmm2_align produce_na_dedup_cram produce_sentdpb_snv_vcf produce_alignstats produce_snv_concordances -p -j 2 -k -T 1"
            }
          ]
        },
        {
          "aligners": [
            "roche"
          ],
          "artifact_registration": null,
          "command_class": "sample_analysis",
          "command_id": "roche_snv_alignstats",
          "compatible_data_modes": [
            "roche_solo"
          ],
          "compatible_platforms": [
            "ROCHE"
          ],
          "datasource": "Roche",
          "dedupers": [
            "na"
          ],
          "description": "Roche aligned BAM HaplotypeCaller and alignment-statistics launch profile.",
          "display_name": "Roche SNV + Alignstats",
          "dryrun_dy_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_rochehc_snv_vcf -p -j 5 -k -n",
          "dy_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_rochehc_snv_vcf -p -j 5 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {},
            "required_source_columns": [
              "ROCHE_BAM",
              "ROCHE_BAM_ALIGNER",
              "ROCHE_BAM_SNV_CALLER"
            ]
          },
          "jobs": 5,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "rochehc"
          ],
          "sv_callers": [],
          "targets": [
            "produce_alignstats",
            "produce_na_dedup_cram",
            "produce_rochehc_snv_vcf"
          ],
          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "tvb_roche_snv_alignstats_5x_1021_dryrun",
              "dryrun_status": "failed",
              "failure_cause": "Dry-run failed while preparing Roche/GATK containers: missing Singularity image /fsx/resources/environments/containers/ubuntu/ip-10-0-0-103/7a424a40c6fd659f4d052893dd3554fa.simg.",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "",
              "live_status": "not_run",
              "notes": "",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T073504Z",
              "status": "failed",
              "tested_command": "bin/day_run produce_alignstats produce_na_dedup_cram produce_rochehc_snv_vcf -p -j 5 -k"
            }
          ]
        },
        {
          "aligners": [
            "sent"
          ],
          "artifact_registration": null,
          "command_class": "sample_analysis",
          "command_id": "hybrid_ilmn_ont_snv",
          "compatible_data_modes": [
            "hybrid_ilmn_ont"
          ],
          "compatible_platforms": [
            "ILMN",
            "ONT"
          ],
          "datasource": "Hybrid ILMN+ONT",
          "dedupers": [
            "dmd"
          ],
          "description": "Hybrid Illumina plus ONT refactored Sentieon HIOMR SNV/SV launch profile.",
          "display_name": "Hybrid ILMN+ONT HIOMR SNV/SV",
          "dryrun_dy_command": "bin/day_run produce_snv_concordances produce_sentdhiomr_sv produce_sentdhiomr_snv_vcf --config 'dedupers=[\"dmd\"]' -p -j 100 -k -n",
          "dy_command": "bin/day_run produce_snv_concordances produce_sentdhiomr_sv produce_sentdhiomr_snv_vcf --config 'dedupers=[\"dmd\"]' -p -j 100 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {},
            "required_source_columns": [
              "ILMN_R1_FQ",
              "ILMN_R2_FQ",
              "ONT_CRAM",
              "ONT_CRAM_ALIGNER",
              "ONT_CRAM_SNV_CALLER"
            ]
          },
          "jobs": 100,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "sentdhiomr"
          ],
          "sv_callers": [
            "sentdhiomr"
          ],
          "targets": [
            "produce_snv_concordances",
            "produce_sentdhiomr_sv",
            "produce_sentdhiomr_snv_vcf"
          ],
          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "tvb_hybrid_ilmn_ont_snv_5x5x_1021_dryrun",
              "dryrun_status": "success",
              "failure_cause": "",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "tvb_hybrid_ilmn_ont_snv_5x5x_1021",
              "live_status": "success",
              "notes": "Live run completed with sentdhiomr SNV/SV and concordance outputs.",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T074001Z",
              "status": "success",
              "tested_command": "bin/day_run produce_snv_concordances produce_sentdhiomr_sv produce_sentdhiomr_snv_vcf --config 'dedupers=[\"dmd\"]' -p -j 100 -k"
            }
          ]
        },
        {
          "aligners": [
            "sent"
          ],
          "artifact_registration": {
            "enabled": true,
            "evidence_manifest_path": "results/day/{genome}/reports/dayoa_evidence_manifest.json",
            "identity": {
              "analysis_euid": "{analysis_id}",
              "assay_id": "",
              "project_euid": "",
              "run_euid": "{analysis_id}",
              "workset_euid": ""
            },
            "include_classifications": [
              "multiqc_html",
              "multiqc_data_json",
              "multiqc_general_stats",
              "multiqc_sources",
              "multiqc_log",
              "custom_mqc_tsv",
              "staging_manifest",
              "benchmark"
            ],
            "include_paths": [
              "results/day/{genome}/reports/DAY_final_multiqc.html",
              "results/day/{genome}/reports/DAY_final_multiqc_data/**",
              "results/day/{genome}/reports/multiqc_inputs/final/manifest.tsv",
              "results/day/{genome}/other_reports/*_mqc.tsv"
            ],
            "multiqc_report_kind": "final",
            "multiqc_version": "1.35",
            "parser_family_hint": "multiqc",
            "require_existing": true
          },
          "command_class": "sample_analysis",
          "command_id": "hybrid_ilmn_ont_snv_kitchensink",
          "compatible_data_modes": [
            "hybrid_ilmn_ont"
          ],
          "compatible_platforms": [
            "ILMN",
            "ONT"
          ],
          "datasource": "Hybrid ILMN+ONT",
          "dedupers": [
            "dmd"
          ],
          "description": "Hybrid Illumina plus ONT refactored Sentieon HIOMR SNV/SV, relatedness, VEP annotation, and final MultiQC launch profile.",
          "display_name": "Hybrid ILMN+ONT HIOMR SNV/SV Kitchen Sink",
          "dryrun_dy_command": "bin/day_run produce_snv_concordances produce_sentdhiomr_sv produce_sentdhiomr_snv_vcf produce_relatedness produce_vep produce_multiqc_all --config 'dedupers=[\"dmd\"]' 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k -n",
          "dy_command": "bin/day_run produce_snv_concordances produce_sentdhiomr_sv produce_sentdhiomr_snv_vcf produce_relatedness produce_vep produce_multiqc_all --config 'dedupers=[\"dmd\"]' 'multiqc_qc={\"enable_tools\":[\"vep\"]}' -p -j 100 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {},
            "required_source_columns": [
              "ILMN_R1_FQ",
              "ILMN_R2_FQ",
              "ONT_CRAM",
              "ONT_CRAM_ALIGNER",
              "ONT_CRAM_SNV_CALLER"
            ]
          },
          "jobs": 100,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "sentdhiomr"
          ],
          "sv_callers": [
            "sentdhiomr"
          ],
          "targets": [
            "produce_snv_concordances",
            "produce_sentdhiomr_sv",
            "produce_sentdhiomr_snv_vcf",
            "produce_relatedness",
            "produce_vep",
            "produce_multiqc_all"
          ],
          "validation_runs": []
        },
        {
          "aligners": [
            "sent"
          ],
          "artifact_registration": null,
          "command_class": "sample_analysis",
          "command_id": "inflection-bjuice-product-v0.1",
          "compatible_data_modes": [
            "hybrid_ilmn_ont"
          ],
          "compatible_platforms": [
            "ILMN",
            "ONT"
          ],
          "datasource": "Hybrid ILMN+ONT",
          "dedupers": [
            "dmd"
          ],
          "description": "Inflection hybrid Illumina plus ONT HIOMR product profile with align, dmd CRAM, SNV, SV, CNV, mito, segdup limited to CYP11B1/NCF1/SMN1, expansionhunter, and concordance targets.",
          "display_name": "Inflection BJuice Product v0.1",
          "dryrun_dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentdhiomr_sv produce_snv_concordances produce_sentdhiomr_snv_vcf produce_sentdhiomr_cnv produce_sentdhiomr_mito produce_sentdhiomr_segdup produce_expansionhunter --config 'sentdhiomr={\"segdup_genes\":\"CYP11B1,NCF1,SMN1\"}' -j 125 -p -k -n",
          "dy_command": "bin/day_run produce_sent_align produce_dmd_dedup_cram produce_sentdhiomr_sv produce_snv_concordances produce_sentdhiomr_snv_vcf produce_sentdhiomr_cnv produce_sentdhiomr_mito produce_sentdhiomr_segdup produce_expansionhunter --config 'sentdhiomr={\"segdup_genes\":\"CYP11B1,NCF1,SMN1\"}' -j 125 -p -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {},
            "required_source_columns": [
              "ILMN_R1_FQ",
              "ILMN_R2_FQ",
              "ONT_CRAM",
              "ONT_CRAM_ALIGNER",
              "ONT_CRAM_SNV_CALLER"
            ]
          },
          "jobs": 125,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "sentdhiomr"
          ],
          "sv_callers": [
            "sentdhiomr"
          ],
          "targets": [
            "produce_sent_align",
            "produce_dmd_dedup_cram",
            "produce_sentdhiomr_sv",
            "produce_snv_concordances",
            "produce_sentdhiomr_snv_vcf",
            "produce_sentdhiomr_cnv",
            "produce_sentdhiomr_mito",
            "produce_sentdhiomr_segdup",
            "produce_expansionhunter"
          ],
          "validation_runs": []
        },
        {
          "aligners": [
            "ug"
          ],
          "artifact_registration": null,
          "command_class": "sample_analysis",
          "command_id": "hybrid_ultima_ont_snv",
          "compatible_data_modes": [
            "hybrid_ug_ont"
          ],
          "compatible_platforms": [
            "ULTIMA",
            "ONT"
          ],
          "datasource": "Hybrid Ultima+ONT",
          "dedupers": [
            "na"
          ],
          "description": "Hybrid Ultima plus ONT refactored modular Sentieon HUOMR SNV launch profile.",
          "display_name": "Hybrid Ultima+ONT HUOMR SNV",
          "dryrun_dy_command": "bin/day_run produce_sentdhuomr_snv_vcf produce_alignstats produce_snv_concordances -p -j 100 -k -n",
          "dy_command": "bin/day_run produce_sentdhuomr_snv_vcf produce_alignstats produce_snv_concordances -p -j 100 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {},
            "required_source_columns": [
              "ULTIMA_CRAM",
              "ULTIMA_CRAM_ALIGNER",
              "ULTIMA_CRAM_SNV_CALLER",
              "ONT_CRAM",
              "ONT_CRAM_ALIGNER",
              "ONT_CRAM_SNV_CALLER"
            ]
          },
          "jobs": 100,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "sentdhuomr"
          ],
          "sv_callers": [],
          "targets": [
            "produce_sentdhuomr_snv_vcf",
            "produce_alignstats",
            "produce_snv_concordances"
          ],
          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "tvb_hybrid_ultima_ont_snv_5x5x_1021_dryrun",
              "dryrun_status": "success",
              "failure_cause": "Live run failed in sentdhuomr_hybrid_select: ModuleNotFoundError: No module named 'sentieon_cli' while resolving files('sentieon_cli.scripts').joinpath('hybrid_select.py').",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "tvb_hybrid_ultima_ont_snv_5x5x_1021",
              "live_status": "failed",
              "notes": "Dry-run passed; live failure was new after the r-suffix command and pass-through staging avoided the prior basename collision.",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "/fsx/staging/staged_external_sequencing_data/remote_stage_20260525T074404Z",
              "status": "failed",
              "tested_command": "bin/day_run produce_sentdhuomr_snv_vcf produce_alignstats produce_snv_concordances -p -j 100 -k"
            }
          ]
        },
        {
          "aligners": [
            "sentcg"
          ],
          "artifact_registration": null,
          "command_class": "sample_analysis",
          "command_id": "complete_genomics_mgi_snv_concordance",
          "compatible_data_modes": [
            "complete_genomics_solo"
          ],
          "compatible_platforms": [
            "CG/MGI"
          ],
          "datasource": "Complete Genomics/MGI",
          "dedupers": [
            "dmd"
          ],
          "description": "Complete Genomics/MGI Sentieon sentcg/dmd/cgt7p launch profile.",
          "display_name": "Complete Genomics/MGI SNV + Concordance",
          "dryrun_dy_command": "bin/day_run produce_sentcg_align produce_dmd_dedup_cram produce_cgt7p_snv_vcf produce_alignstats produce_snv_concordances -p -j 20 -k -T 1 --retries 0 --rerun-incomplete --keep-incomplete -n",
          "dy_command": "bin/day_run produce_sentcg_align produce_dmd_dedup_cram produce_cgt7p_snv_vcf produce_alignstats produce_snv_concordances -p -j 20 -k -T 1 --retries 0 --rerun-incomplete --keep-incomplete",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "sample_manifest",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {},
            "required_source_columns": [
              "CG_R1_FQ",
              "CG_R2_FQ"
            ]
          },
          "jobs": 20,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": false,
          "requires_staging": true,
          "runtime_parameters": {},
          "snv_callers": [
            "cgt7p"
          ],
          "sv_callers": [],
          "targets": [
            "produce_sentcg_align",
            "produce_dmd_dedup_cram",
            "produce_cgt7p_snv_vcf",
            "produce_alignstats",
            "produce_snv_concordances"
          ],
          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "",
              "dryrun_status": "blocked",
              "failure_cause": "Blocked before dry-run because the candidate mate pair was not verified: _386_1 was 90,600,002,744 bytes, _386_2 was 10,794,018,984 bytes, and nearby _388_2 was 97,844,317,264 bytes.",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "",
              "live_status": "blocked",
              "notes": "",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "docs/plans/20260525T063158Z_tstver411b_inputs/complete_genomics_mgi_hg003_candidate_blocked.tsv",
              "status": "blocked",
              "tested_command": "bin/day_run produce_sentcg_align produce_dmd_dedup_cram produce_cgt7p_snv_vcf produce_alignstats produce_snv_concordances -p -j 20 -k -T 1 --retries 0 --rerun-incomplete --keep-incomplete"
            }
          ]
        },
        {
          "aligners": [],
          "artifact_registration": null,
          "command_class": "run_analysis",
          "command_id": "illumina_run_qc",
          "compatible_data_modes": [
            "run_directory_mount"
          ],
          "compatible_platforms": [
            "ILMN"
          ],
          "datasource": "Illumina",
          "dedupers": [],
          "description": "Illumina run-folder QC from a mounted or explicit S3 run context.",
          "display_name": "Illumina Run QC",
          "dryrun_dy_command": "bin/day_run produce_illumina_run_qc -p -j 5 -k -n",
          "dy_command": "bin/day_run produce_illumina_run_qc -p -j 5 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "run_context",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {
              "PLATFORM": "ILMN"
            },
            "required_source_columns": []
          },
          "jobs": 5,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": true,
          "requires_staging": false,
          "runtime_parameters": {
            "run_context_file": "config/runs.tsv",
            "samples_table": ".test_data/data/samples.tsv",
            "units_table": ".test_data/data/units.tsv"
          },
          "snv_callers": [],
          "sv_callers": [],
          "targets": [
            "produce_illumina_run_qc"
          ],
          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "tvb_illumina_run_qc_1021_dryrun",
              "dryrun_status": "failed",
              "failure_cause": "Dry-run failed: WorkflowError reported config/units.tsv was not found and requested config/units.tsv or --config units_table=/path/to/units.tsv.",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "",
              "live_status": "not_run",
              "notes": "",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "/fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/",
              "status": "failed",
              "tested_command": "bin/day_run produce_illumina_run_qc -p -j 5 -k --config run_context_file=config/runs.tsv samples_table=.test_data/data/samples.tsv units_table=.test_data/data/units.tsv"
            }
          ]
        },
        {
          "aligners": [],
          "artifact_registration": null,
          "command_class": "run_analysis",
          "command_id": "illumina_bclconvert",
          "compatible_data_modes": [
            "run_directory_mount"
          ],
          "compatible_platforms": [
            "ILMN"
          ],
          "datasource": "Illumina",
          "dedupers": [],
          "description": "Illumina demultiplexing through the pinned nf-core/bclconvert 4.0.3 container from a mounted run directory, with generated units table, demux metric TSVs, and focused BCL Convert MultiQC. This command does not run FastQC.",
          "display_name": "Illumina nf-core BCL Convert",
          "dryrun_dy_command": "bin/day_run produce_bclconvert_fastqs_and_metrics -p -j 20 -k -n",
          "dy_command": "bin/day_run produce_bclconvert_fastqs_and_metrics -p -j 20 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "run_context",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {
              "PLATFORM": "ILMN"
            },
            "required_source_columns": []
          },
          "jobs": 20,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": true,
          "requires_staging": false,
          "runtime_parameters": {
            "run_context_file": "config/runs.tsv",
            "samples_table": ".test_data/data/bclconvert/samples.tsv",
            "units_table": ".test_data/data/bclconvert/units.tsv"
          },
          "snv_callers": [],
          "sv_callers": [],
          "targets": [
            "produce_bclconvert_fastqs_and_metrics"
          ],
          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "tvb_illumina_bclconvert_1021_dryrun",
              "dryrun_status": "failed",
              "failure_cause": "Dry-run failed: WorkflowError reported no read pairs specified for analysis unit 20260514_LH01106_0009_B23TVLGLT4.",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "",
              "live_status": "not_run",
              "notes": "",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "/fsx/run_dir_mounts/20260514_LH01106_0009_B23TVLGLT4/",
              "status": "failed",
              "tested_command": "bin/day_run produce_bclconvert_fastqs_and_metrics -p -j 20 -k --config run_context_file=config/runs.tsv samples_table=.test_data/data/bclconvert/samples.tsv units_table=.test_data/data/bclconvert/units.tsv"
            }
          ]
        },
        {
          "aligners": [],
          "artifact_registration": null,
          "command_class": "run_analysis",
          "command_id": "illumina_run_qc_bclconvert",
          "compatible_data_modes": [
            "run_directory_mount"
          ],
          "compatible_platforms": [
            "ILMN"
          ],
          "datasource": "Illumina",
          "dedupers": [],
          "description": "Mounted Illumina run-folder QC plus demultiplexing through the pinned nf-core/bclconvert 4.0.3 container, generated units, demux metric TSVs, and focused BCL Convert MultiQC in one run-analysis output tree. This command does not run FastQC.",
          "display_name": "Illumina Run QC + nf-core BCL Convert",
          "dryrun_dy_command": "bin/day_run produce_illumina_run_qc_and_bclconvert -p -j 20 -k -n",
          "dy_command": "bin/day_run produce_illumina_run_qc_and_bclconvert -p -j 20 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "run_context",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {
              "PLATFORM": "ILMN"
            },
            "required_source_columns": []
          },
          "jobs": 20,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": true,
          "requires_staging": false,
          "runtime_parameters": {
            "run_context_file": "config/runs.tsv",
            "samples_table": ".test_data/data/bclconvert/samples.tsv",
            "units_table": ".test_data/data/bclconvert/units.tsv"
          },
          "snv_callers": [],
          "sv_callers": [],
          "targets": [
            "produce_illumina_run_qc_and_bclconvert"
          ],
          "validation_runs": []
        },
        {
          "aligners": [],
          "artifact_registration": null,
          "command_class": "run_analysis",
          "command_id": "ont_run_qc",
          "compatible_data_modes": [
            "run_directory_mount"
          ],
          "compatible_platforms": [
            "ONT"
          ],
          "datasource": "ONT",
          "dedupers": [],
          "description": "ONT mounted run-folder QC plus demux FASTQ SeqKit/Nanoq/NanoStat/NanoPlot outputs and focused demux MultiQC in one run-analysis output tree.",
          "display_name": "ONT Run QC + Demux MultiQC",
          "dryrun_dy_command": "bin/day_run produce_ont_run_qc_and_demux_multiqc -p -j 5 -k -n",
          "dy_command": "bin/day_run produce_ont_run_qc_and_demux_multiqc -p -j 5 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "run_context",
          "input_requirements": {
            "accepted_source_column_sets": [],
            "required_run_context_values": {
              "PLATFORM": "ONT"
            },
            "required_source_columns": []
          },
          "jobs": 5,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
          "repository": "daylily-omics-analysis",
          "requires_run_mount": true,
          "requires_staging": false,
          "runtime_parameters": {
            "run_context_file": "config/runs.tsv",
            "samples_table": ".test_data/data/samples.tsv",
            "units_table": ".test_data/data/units.tsv"
          },
          "snv_callers": [],
          "sv_callers": [],
          "targets": [
            "produce_ont_run_qc_and_demux_multiqc"
          ],
          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "tvb_ont_run_qc_1021_dryrun",
              "dryrun_status": "failed",
              "failure_cause": "Dry-run failed: WorkflowError reported config/units.tsv was not found and requested config/units.tsv or --config units_table=/path/to/units.tsv.",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "",
              "live_status": "not_run",
              "notes": "",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "/fsx/run_dir_mounts/20260513_ONT_HG003/",
              "status": "failed",
              "tested_command": "bin/day_run produce_ont_run_qc -p -j 5 -k --config run_context_file=config/runs.tsv samples_table=.test_data/data/samples.tsv units_table=.test_data/data/units.tsv"
            }
          ]
        },
        {
          "aligners": [],
          "artifact_registration": null,
          "command_class": "run_analysis",
          "command_id": "ultima_run_qc",
          "compatible_data_modes": [
            "run_directory_mount"
          ],
          "compatible_platforms": [
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          ],
          "datasource": "Ultima",
          "dedupers": [],
          "description": "Ultima run-folder QC from a mounted run context.",
          "display_name": "Ultima Run QC",
          "dryrun_dy_command": "bin/day_run produce_ultima_run_qc -p -j 5 -k -n",
          "dy_command": "bin/day_run produce_ultima_run_qc -p -j 5 -k",
          "genome": "hg38_broad",
          "git_tag": "2.0.23",
          "input_contract": "run_context",
          "input_requirements": {
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            "required_run_context_values": {
              "PLATFORM": "ULTIMA"
            },
            "required_source_columns": []
          },
          "jobs": 5,
          "launcher": "workflow_launch",
          "no_containerized": false,
          "optional_features": {},
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          "requires_run_mount": true,
          "requires_staging": false,
          "runtime_parameters": {
            "run_context_file": "config/runs.tsv",
            "samples_table": ".test_data/data/samples.tsv",
            "units_table": ".test_data/data/units.tsv"
          },
          "snv_callers": [],
          "sv_callers": [],
          "targets": [
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          "validation_runs": [
            {
              "cluster": "tstVer4-1-1b",
              "dayec_commit": "012a3b5b30d2e69a07aa80dd4c224ad1ee26d3a4",
              "dayec_tag": "4.1.3",
              "dayoa_commit": "c2ffe93f246ff19c346f0a99e04fddc9e2712ff3",
              "dayoa_tag": "1.0.21",
              "dryrun_analysis_id": "tvb_ultima_run_qc_1021_dryrun",
              "dryrun_status": "failed",
              "failure_cause": "Dry-run failed: WorkflowError reported config/units.tsv was not found and requested config/units.tsv or --config units_table=/path/to/units.tsv.",
              "generated_at": "2026-05-25T20:04:39Z",
              "ledger_path": "docs/plans/20260525T063158Z_tstver411b_dayoa_catalog_recipe_validation_ledger.md",
              "live_analysis_id": "",
              "live_status": "not_run",
              "notes": "",
              "region": "us-west-2",
              "region_az": "us-west-2d",
              "report_path": "docs/tstver411b_command_catalog_test_results.md",
              "run_id": "tstver411b_dayoa_catalog_recipe_validation",
              "stage_or_context": "/fsx/run_dir_mounts/602221-20260417_2346/",
              "status": "failed",
              "tested_command": "bin/day_run produce_ultima_run_qc -p -j 5 -k --config run_context_file=config/runs.tsv samples_table=.test_data/data/samples.tsv units_table=.test_data/data/units.tsv"
            }
          ]
        }
      ],
      "default_ref": "2.0.23",
      "description": "Primary whole genome and multiomics workflows.",
      "display_name": "Daylily Omics Analysis",
      "https_url": "https://github.com/Daylily-Informatics/daylily-omics-analysis.git",
      "relative_path": "daylily-omics-analysis",
      "ssh_url": "git@github.com:Daylily-Informatics/daylily-omics-analysis.git"
    }
  }
}
