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add second sample to multiqc-data fixture and deliverables.yaml
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@peterpru
peterpru committed Sep 11, 2024
1 parent ece8361 commit e913382
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222 changes: 221 additions & 1 deletion tests/fixtures/analysis/raredisease/multiqc_data.json
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Original file line number Diff line number Diff line change
Expand Up @@ -202,7 +202,227 @@
"het_ratio_sex_check": 0.03753,
"predicted_sex_sex_check": "female",
"error_sex_check": "True"
},
"ADM2_1": {
"percent_gc": 40.0,
"avg_sequence_length": 151.0,
"median_sequence_length": 151,
"total_sequences": 300008747.0,
"percent_duplicates": 8.309768884963006,
"percent_fails": 0.0
},
"ADM2_2": {
"percent_gc": 41.0,
"avg_sequence_length": 151.0,
"median_sequence_length": 151,
"total_sequences": 299990878.0,
"percent_duplicates": 9.121697870826623,
"percent_fails": 0.0
}
},
{
"ADM2": {
"BAIT_SET": "home_bait",
"BAIT_TERRITORY": 77043000.0,
"BAIT_DESIGN_EFFICIENCY": 0.471991,
"ON_BAIT_BASES": 2168131962.0,
"NEAR_BAIT_BASES": 3025317220.0,
"OFF_BAIT_BASES": 82119739945.0,
"PCT_SELECTED_BASES": 0.059481,
"PCT_OFF_BAIT": 0.940519,
"ON_BAIT_VS_SELECTED": 0.417474,
"MEAN_BAIT_COVERAGE": 28.141842,
"PCT_USABLE_BASES_ON_BAIT": 0.024739,
"PCT_USABLE_BASES_ON_TARGET": 0.010185,
"FOLD_ENRICHMENT": 1.01123,
"HS_LIBRARY_SIZE": 209575187.0,
"HS_PENALTY_10X": 116.595122,
"HS_PENALTY_20X": 119.154837,
"HS_PENALTY_30X": 121.636986,
"HS_PENALTY_40X": 124.506969,
"HS_PENALTY_50X": 127.345926,
"HS_PENALTY_100X": 145.589715,
"TARGET_TERRITORY": 36363631.0,
"GENOME_SIZE": 3137454505.0,
"TOTAL_READS": 582127482.0,
"PF_READS": 582127482.0,
"PF_BASES": 87639826450.0,
"PF_UNIQUE_READS": 554469972.0,
"PF_UQ_READS_ALIGNED": 554378136.0,
"PF_BASES_ALIGNED": 87313189127.0,
"PF_UQ_BASES_ALIGNED": 83169064702.0,
"ON_TARGET_BASES": 892599615.0,
"PCT_PF_READS": 1.0,
"PCT_PF_UQ_READS": 0.952489,
"PCT_PF_UQ_READS_ALIGNED": 0.999834,
"MEAN_TARGET_COVERAGE": 24.546493,
"MEDIAN_TARGET_COVERAGE": 27.0,
"MAX_TARGET_COVERAGE": 293.0,
"MIN_TARGET_COVERAGE": 0.0,
"ZERO_CVG_TARGETS_PCT": 0.011192,
"PCT_EXC_DUPE": 0.047463,
"PCT_EXC_ADAPTER": 0.0,
"PCT_EXC_MAPQ": 0.046112,
"PCT_EXC_BASEQ": 0.011212,
"PCT_EXC_OVERLAP": 0.046622,
"PCT_EXC_OFF_TARGET": 0.838374,
"PCT_TARGET_BASES_1X": 0.986489,
"PCT_TARGET_BASES_2X": 0.985327,
"PCT_TARGET_BASES_10X": 0.9692,
"PCT_TARGET_BASES_20X": 0.800972,
"PCT_TARGET_BASES_30X": 0.228001,
"PCT_TARGET_BASES_40X": 0.011174,
"PCT_TARGET_BASES_50X": 0.001188,
"PCT_TARGET_BASES_100X": 0.000148,
"PCT_TARGET_BASES_250X": 2e-06,
"PCT_TARGET_BASES_500X": 0.0,
"PCT_TARGET_BASES_1000X": 0.0,
"PCT_TARGET_BASES_2500X": 0.0,
"PCT_TARGET_BASES_5000X": 0.0,
"PCT_TARGET_BASES_10000X": 0.0,
"PCT_TARGET_BASES_25000X": 0.0,
"PCT_TARGET_BASES_50000X": 0.0,
"PCT_TARGET_BASES_100000X": 0.0,
"AT_DROPOUT": 0.061814,
"GC_DROPOUT": 3.395193,
"HET_SNP_SENSITIVITY": 0.984192,
"HET_SNP_Q": 18.0,
"SAMPLE": "",
"LIBRARY": "",
"READ_GROUP": ""
}
},
{
"ADM2": {
"total_count": 272277544,
"meansum": 90261639990.04478,
"total_pairs": 272728731.0,
"summed_mean": 330.957577,
"summed_median": 327
}
},
{
"ADM2": {
"GENOME_TERRITORY": 2858674663.0,
"MEAN_COVERAGE": 25.002304,
"SD_COVERAGE": 7.564118,
"MEDIAN_COVERAGE": 27.0,
"MAD_COVERAGE": 4.0,
"PCT_EXC_ADAPTER": 3e-06,
"PCT_EXC_MAPQ": 0.028096,
"PCT_EXC_DUPE": 0.041988,
"PCT_EXC_UNPAIRED": 8.8e-05,
"PCT_EXC_BASEQ": 0.012141,
"PCT_EXC_OVERLAP": 0.046242,
"PCT_EXC_CAPPED": 0.004331,
"PCT_EXC_TOTAL": 0.13289,
"PCT_1X": 0.988269,
"PCT_5X": 0.984082,
"PCT_10X": 0.969498,
"PCT_15X": 0.926194,
"PCT_20X": 0.82183,
"PCT_25X": 0.5636,
"PCT_30X": 0.247956,
"PCT_40X": 0.012271,
"PCT_50X": 0.001739,
"PCT_60X": 0.001019,
"PCT_70X": 0.000676,
"PCT_80X": 0.000491,
"PCT_90X": 0.000369,
"PCT_100X": 0.000274,
"FOLD_80_BASE_PENALTY": 1.250115,
"FOLD_90_BASE_PENALTY": 1.562644,
"FOLD_95_BASE_PENALTY": 2.083525
}
},
{
"ADM2": {
"total_reads": 582127482,
"mapped_reads": 582035646,
"general_error_rate": 0.41000000000000003,
"mean_coverage": 27.8391,
"percentage_aligned": 99.98422407413501
},
"ADM2_qualimap": {
"median_coverage": 28,
"median_insert_size": 328,
"avg_gc": 41.33062822983583,
"1_x_pc": 92.29551680782062,
"5_x_pc": 92.09514089830603,
"10_x_pc": 91.13522460463534,
"30_x_pc": 40.58657229836071,
"50_x_pc": 0.8020039799748427
}
},
{
"ADM2_mosdepth": {
"1_x_pc": 92.0,
"5_x_pc": 92.0,
"10_x_pc": 91.0,
"30_x_pc": 25.0,
"50_x_pc": 1.0,
"median_coverage": 27
}
},
{
"ADM2": {
"family_id": "raredisease_case_enough_reads",
"paternal_id": 0.0,
"maternal_id": 0.0,
"sex": 2.0,
"phenotype": 1.0,
"het_call_rate": 1.0,
"het_ratio": 0.46773785425101216,
"het_mean_depth": 24.91599190283401,
"het_idr_baf": 0.265993265993266,
"ancestry-prediction": "EUR",
"PC1": -0.4272191936528722,
"PC2": -1.3373174157150056,
"PC3": -0.4438895963046335,
"sex_het_ratio": 0.03752899009065992,
"depth_outlier_het_check": "False",
"het_count_het_check": 3697.0,
"het_ratio_het_check": 0.4677,
"idr_baf_het_check": 0.266,
"mean_depth_het_check": 24.92,
"median_depth_het_check": 24.0,
"p10_het_check": 0.3636,
"p90_het_check": 0.6296,
"sampled_sites_het_check": 7864.0,
"call_rate_het_check": 1.0,
"ancestry-prediction_het_check": "EUR",
"ancestry-prob_het_check": 0.9956,
"PC1_het_check": -0.4272,
"PC2_het_check": -1.337,
"PC3_het_check": -0.4439,
"PC4_het_check": -0.8576,
"ped_sex_sex_check": "female",
"hom_ref_count_sex_check": 4313.0,
"het_count_sex_check": 178.0,
"hom_alt_count_sex_check": 4743.0,
"het_ratio_sex_check": 0.03753,
"predicted_sex_sex_check": "female",
"error_sex_check": "True"
}
}
],
"report_saved_raw_data": {
"multiqc_peddy": {
"ADM1-ADM2": {
"rel_ped_check": 0.4917,
"hets_a_ped_check": 3624.0,
"hets_b_ped_check": 3704.0,
"shared_hets_ped_check": 1808.0,
"ibs0_ped_check": 13.0,
"ibs2_ped_check": 4164.0,
"n_ped_check": 7886.0,
"pedigree_parents_ped_check": "True",
"pedigree_relatedness_ped_check": 0.5,
"predicted_parents_ped_check": "True",
"parent_error_ped_check": "False",
"sample_duplication_error_ped_check": "False",
"rel_difference_ped_check": 0.008278
}
}
]
}
}
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