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Output files

Output in the results folder (default results/) in the standard case when publish_all = false:

├── dump_versions
│   └── software_versions.yml
├── pipeline_info
│   ├── execution_report_2024-07-11-11-54-27.html
│   ├── execution_timeline_2024-07-11-11-54-27.html
│   └── execution_trace_2024-07-11-11-54-27.txt
├── regenie_aggregate_summary_statistics
│   └── aggregated_regenie_results_STATUS.tsv
├── run_fishers_test_using_rvtests
│   ├── STATUS_mask_LoF_recessive_false_avt_output.DominantFisherExact.assoc
│   ├── STATUS_mask_LoF_recessive_false_avt_output.log
│   ├── STATUS_mask_missense_recessive_false_avt_output.DominantFisherExact.assoc
│   ├── STATUS_mask_missense_recessive_false_avt_output.log
│   ├── STATUS_mask_synonymous_recessive_false_avt_output.DominantFisherExact.assoc
│   └── STATUS_mask_synonymous_recessive_false_avt_output.log
├── saige_aggregate_summary_statistics
│   ├── aggregated_saige_set_results_STATUS.tsv
│   └── aggregated_saige_single_variant_results_STATUS.tsv
└── validate_input_files
    ├── exclusion_data_type.txt
    ├── validated_annotation_data_list.tsv
    ├── validated_genomic_data_list.tsv
    ├── validated_user_exclusion_file.tsv
    ├── validated_user_region_file.tsv
    ├── validation_errors.txt
    └── workflow_internal_initial_cohort_file.tsv

if publish_all = true, all intermediate files will be published in the results folder, organised in sub-folders in a way similar to what is shown above.

Association output files

# Aggregated association output (all annotation labels in the same file)
aggregated_regenie_results_<phenotype>.tsv
aggregated_saige_set_results_<phenotype>.tsv
aggregated_saige_single_variant_results_<phenotype>.tsv

# Rvtests
<phenotype>_mask_<annotationLabel>_<testType>_<suffix>.DominantFisherExact.assoc
<phenotype>_mask_<annotationLabel>_<testType>_<suffix>.log

See individual association tool documentation for interpretation of association output:

SAIGE-GENE

regenie

Rvtests/Fisher's test