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runRegenieStandardPipeline

runRegenieStandardPipeline.Rd

Submit the Regenie unmodifiable standard pipeline via internal standard-pipelines API. Creates phenotype + description files locally, uploads them to SANDBOX_RED/CO2_temp//<run_tag>/ (using RED_BUCKET for gsutil), builds WDL-style input JSON referencing SANDBOX_RED paths, and submits the workflow. Users are allowed to add additional covariates using a dataframe of columns for each additional covariate.

Usage

runRegenieStandardPipeline(
  connection_sandboxAPI,
  standard_pipeline_id = "5718330904150016",
  cases_finngenids,
  controls_finngenids,
  phenotype_name,
  phenotype_description,
  covariates =
    "SEX_IMPUTED,AGE_AT_DEATH_OR_END_OF_FOLLOWUP,PC{1:10},IS_FINNGEN2_CHIP,BATCH_DS1_BOTNIA_Dgi_norm,BATCH_DS10_FINRISK_Palotie_norm,BATCH_DS11_FINRISK_PredictCVD_COROGENE_Tarto_norm,BATCH_DS12_FINRISK_Summit_norm,BATCH_DS13_FINRISK_Bf_norm,BATCH_DS14_GENERISK_norm,BATCH_DS15_H2000_Broad_norm,BATCH_DS16_H2000_Fimm_norm,BATCH_DS17_H2000_Genmets_norm_relift,BATCH_DS18_MIGRAINE_1_norm_relift,BATCH_DS19_MIGRAINE_2_norm,BATCH_DS2_BOTNIA_T2dgo_norm,BATCH_DS20_SUPER_1_norm_relift,BATCH_DS21_SUPER_2_norm_relift,BATCH_DS22_TWINS_1_norm,BATCH_DS23_TWINS_2_norm_nosymmetric,BATCH_DS24_SUPER_3_norm,BATCH_DS25_BOTNIA_Regeneron_norm,BATCH_DS26_DIREVA_norm,BATCH_DS27_NFBC66_norm,BATCH_DS28_NFBC86_norm,BATCH_DS3_COROGENE_Sanger_norm,BATCH_DS4_FINRISK_Corogene_norm,BATCH_DS5_FINRISK_Engage_norm,BATCH_DS6_FINRISK_FR02_Broad_norm_relift,BATCH_DS7_FINRISK_FR12_norm,BATCH_DS8_FINRISK_Finpcga_norm,BATCH_DS9_FINRISK_Mrpred_norm",
  extra_covariates_df = NULL,
  test = "additive",
  is_binary = "true",
  endpoint_path = "v2/standard-pipelines",
  timeout_sec = 300
)

Arguments

connection_sandboxAPI

List-like object containing base_url, token, conn_status_tibble

standard_pipeline_id

Standard pipeline id of the pipeline to be used

cases_finngenids

Character vector of FINNGENIDs for cases

controls_finngenids

Character vector of FINNGENIDs for controls

phenotype_name

Phenotype column name (must start with a letter; letters/numbers/_)

phenotype_description

Single string description written to phenodescription file (1 line)

covariates

Optional comma-separated covariate string of the standard FinnGen covariates

extra_covariates_df

data.frame with FID/IID + extra covariate columns

test

Genetic model test string, Default: "additive"

is_binary

String "true"/"false" to specify binary or quantitative GWAS analysis type, Default: "true"

endpoint_path

internal API path, Default: "v2/standard-pipelines"

timeout_sec

httr timeout seconds, Default: 300

Value

list(status, http_status, workflow_id, content, temp_files, sandbox_paths_used, upload_logs)