# Import and deposit

NOTE

This documentation is a work in progress and is incomplete.

Please contact developers for more details.

Options for import or deposit of variants and/or samples.

# Import

[TODO]

  • File: ella_config.yml (set by ELLA_CONFIG env variable)
  • Key: import
Subkey Explanation Values
automatic_deposit_with_sample_id [TODO] True / False
preimport_script [TODO] [path]

# Deposit

Processes that should be run when new analyses are deposited into ELLA, configured per user group. See /src/vardb/testdata/usergroups.json for examples.

  • File: usergroups.json (see user groups)
  • Key: config.deposit.analysis
Subkey Explanation Values
pattern What analysis name should be matched for this configuration block (e.g. search for user group specific parts in analysis names). [regex]
postprocess Processes that should be applied after analyses have been loaded into ELLA. analysis_not_ready_warnings: Places analyses that includes variants that need verification or have warnings generated by the pipeline in the "Not ready" section on the OVERVIEW page.
analysis_finalize_without_findings: Analyses that have no variants that need further work (only benign, no technical issues) are automatically finalized, without any user interaction.
analysis_tag_all_classified: Adds an OVERVIEW comment automatically for the following conditions: ALL CLASSIFIED when all variants are already classified and still valid; NO VARIANTS when there are no non-filtered variants.
prefilter Whether to prefilter this analysis (e.g. high-frequent variants), useful for limiting resource use for large gene panels. Note that these will not be available in the "FILTERED" variants list. true/false

Note that only one user group and one configuration can match any given analysis name.

# Default import gene panel

Gene panel that should be pre-selected when importing data through the IMPORT function, configured per user group. See /src/vardb/testdata/usergroups.json for examples. :

  • File: usergroups.json (see user groups)
  • Key: default_import_genepanel
  • Value: [gene panel name], [version]
Last Updated: 6/22/2020, 1:34:14 PM