Open Yu-jinKim opened 1 month ago
240524_393:
dx cat file-Gk8vPyj4ppB5B49Yvxg0b3bY | jq ".report_saved_raw_data | keys"
[
"multiqc_bcl2fastq_bylane",
"multiqc_bcl2fastq_bysample",
"multiqc_fastqc",
"multiqc_general_stats",
"multiqc_happy_indel_data",
"multiqc_happy_snp_data",
"multiqc_het-hom_table",
"multiqc_picard_HsMetrics",
"multiqc_samtools_flagstat",
"multiqc_sentieon_AlignmentSummaryMetrics",
"multiqc_sentieon_insertSize",
"multiqc_somalier_table",
"multiqc_verifybamid",
"picard_histogram",
"picard_histogram_1",
"picard_histogram_2"
]
240415_352:
dx cat file-GjPBQKQ42gy47gVxqpQvz5zg | jq '.report_saved_raw_data | keys'
[
"multiqc_bcl2fastq_bylane",
"multiqc_bcl2fastq_bysample",
"multiqc_fastqc",
"multiqc_general_stats",
"multiqc_happy_indel_data",
"multiqc_happy_snp_data",
"multiqc_het-hom_analysis",
"multiqc_picard_HsMetrics",
"multiqc_samtools_flagstat",
"multiqc_sentieon_AlignmentSummaryMetrics",
"multiqc_sentieon_insertSize",
"multiqc_somalier_sex_check",
"multiqc_verifybamid"
]
Somalier had its name changed as well
Comparing the config files used in those jobs:
diff -sy --suppress-common-lines <(dx cat file-Gj81GKQ46f9Kgb0fPB56Jzkk) <(dx cat file-GV55qpj47f086YFQb47B5Gg4)
info: "detects sample contamination." | info: "detects sample contamination"
picard_hsmetrics_table: # Specify the order in which tabl <
BAIT_DESIGN_EFFICIENCY: 780 <
FOLD_80_BASE_PENALTY: 790 <
FOLD_ENRICHMENT: 800 <
HET_SNP_Q: 810 <
HET_SNP_SENSITIVITY: 820 <
MAX_TARGET_COVERAGE: 830 <
MEAN_BAIT_COVERAGE: 840 <
MEAN_TARGET_COVERAGE: 850 <
MEDIAN_TARGET_COVERAGE: 860 <
NEAR_BAIT_BASES: 870 <
OFF_BAIT_BASES: 880 <
ON_BAIT_BASES: 890 <
ON_BAIT_VS_SELECTED: 900 <
ON_TARGET_BASES: 910 <
PCT_USABLE_BASES_ON_BAIT: 920 <
PCT_USABLE_BASES_ON_TARGET: 930 <
PF_BASES_ALIGNED: 940 <
PF_READS: 950 <
PF_UNIQUE_READS: 960 <
PF_UQ_BASES_ALIGNED: 970 <
PF_UQ_READS_ALIGNED: 980 <
ZERO_CVG_TARGETS_PCT: 990 <
PCT_SELECTED_BASES: 1000 <
- 20 # for conditional table f | - 20 # for conditional tabl
<
<
custom_table_header_config: <
picard_hsmetrics_table: <
FOLD_80_BASE_PENALTY: <
format: "{:,.3f}"
The naming of the key in the report_saved_raw_data is done here: https://github.com/MultiQC/MultiQC/blob/v1.14/multiqc/modules/custom_content/custom_content.py#L367 and it looks like it uses the pconfig.id to name the key. The 2 config file are identical in their pconfig.id which doesn't make sense since the keys are different in the JSON file
Previously, we were using v1.11 of MultiQC: file-GF3PxgQ433Gqv1Q029Gjzjfv
The docker image for v1.14 of MultiQC was created in March 27th 2024 in 001_Reference: file-Gj22pvQ433Gk8Y6JJXy5J73Y
v1.11 was using the section name to name the output: https://github.com/MultiQC/MultiQC/blob/v1.11/multiqc/modules/custom_content/custom_content.py#L345 and https://github.com/MultiQC/MultiQC/blob/v1.11/multiqc/modules/custom_content/custom_content.py#L363
v1.14 uses the pconfig.id to name the output: https://github.com/MultiQC/MultiQC/blob/v1.14/multiqc/modules/custom_content/custom_content.py#L367
Hence the discrepancy.
002_240524_A01303_0393_AH7YWCDRX5_CEN
doesn't havemultiqc_het-hom_analysis
inreport_saved_raw_data
as expected. Instead it hasmultiqc_het-hom_table
. No idea why couldn't find any indication in the multiqc config for CEN of a change