## ----include = FALSE-----------------------------------------------------
knitr::opts_chunk$set(
    eval =  AnVIL::gcloud_exists(), collapse = TRUE, cache = TRUE
)
options(width=75)

## ----eval = FALSE--------------------------------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE))
#      install.packages("BiocManager", repos = "https://cran.r-project.org")
#  BiocManager::install("AnVIL")

## ----message = FALSE, eval = TRUE, cache = FALSE-------------------------
library(AnVIL)

## ----workspace-----------------------------------------------------------
#  avworkspace("bioconductor-rpci-anvil/Bioconductor-Workflow-DESeq2")

## ----workflows-----------------------------------------------------------
#  avworkflows()

## ----workflow------------------------------------------------------------
#  avworkflow("bioconductor-rpci-anvil/AnVILBulkRNASeq")

## ----configuration-------------------------------------------------------
#  config <- avworkflow_configuration_get()
#  config

## ----inputs_outputs------------------------------------------------------
#  inputs <- avworkflow_configuration_inputs(config)
#  inputs
#  
#  outputs <- avworkflow_configuration_outputs(config)
#  outputs

## ----change_input--------------------------------------------------------
#  inputs <-
#      inputs |>
#      mutate(
#          attribute = ifelse(
#              name == "salmon.transcriptome_index_name",
#              '"new_index_name"',
#              attribute
#          )
#      )
#  inputs

## ----update_config-------------------------------------------------------
#  new_config <- avworkflow_configuration_update(config, inputs)
#  new_config

## ----set_config----------------------------------------------------------
#  avworkflow_configuration_set(new_config)

## ----set_config_not_dry--------------------------------------------------
#  ## avworkflow_configuration_set(new_config, dry = FALSE)

## ----entityName----------------------------------------------------------
#  entityName <- avtable("participant_set") |>
#      pull(participant_set_id) |>
#      head(1)
#  avworkflow_run(new_config, entityName)

## ----run_not_dry---------------------------------------------------------
#  ## avworkflow_run(new_config, entityName, dry = FALSE)

## ----checking_workflow---------------------------------------------------
#  avworkflow_jobs()

## ----stop_workflow-------------------------------------------------------
#  avworkflow_stop() # dry = FALSE to stop
#  
#  avworkflow_jobs()

## ----files---------------------------------------------------------------
#  submissionId <- "fb8e35b7-df5d-49e6-affa-9893aaeebf37"
#  avworkflow_files(submissionId)

## ----localize------------------------------------------------------------
#  avworkflow_localize(
#      submissionId,
#      type = "output"
#      ## dry = FALSE to localize
#  )

## ----eval = FALSE--------------------------------------------------------
#  avworkspace("bioconductor-rpci-yubo/Rcollectlworkflowh5ad")
#  submissionId <- "9385fd75-4cb7-470f-9e07-1979e2c8f193"
#  info_1 <- avworkflow_info(submissionId)

## ----message=FALSE, warning=FALSE----------------------------------------
#  info_file_1 <- system.file(package = "AnVIL", "extdata", "avworkflow_info_1.rds")
#  info_1 <- readRDS(info_file_1)
#  
#  ## view result of avworkflow_info()
#  info_1

## ------------------------------------------------------------------------
#  info_1 |>
#      select(workflowId, status, inputs, outputs)

## ------------------------------------------------------------------------
#  info_1 |>
#      select(workflowId, status, inputs) |>
#      tidyr::unnest_wider(inputs)

## ------------------------------------------------------------------------
#  info_1 |>
#      select(workflowId, outputs) |>
#      tidyr::unnest_wider(outputs) |>
#      tidyr::unnest_longer(starts_with("Rcollectl"), keep_empty = TRUE)

## ----eval = FALSE--------------------------------------------------------
#  submissionId <- "35280de1-42d8-492b-aa8c-5feff984bffa"
#  info_2 <- avworkflow_info(submissionId)

## ----message=FALSE, warning=FALSE----------------------------------------
#  info_file_2 <- system.file(package = "AnVIL", "extdata", "avworkflow_info_2.rds")
#  info_2 <- readRDS(info_file_2)
#  info_2

## ----message=FALSE, warning=FALSE----------------------------------------
#  info_2 |>
#      select(workflowId, outputs) |>
#      tidyr::unnest_wider(outputs)

## ------------------------------------------------------------------------
#  output_files <-
#      info_2 |>
#      select(workflowId, outputs) |>
#      tidyr::unnest_wider(outputs) |>
#      select(RcollectlWorkflowDelayedArrayParameters.Rcollectl_result) |>
#      tidyr::unnest_longer(
#          "RcollectlWorkflowDelayedArrayParameters.Rcollectl_result"
#      )
#  output_files

## ------------------------------------------------------------------------
#  output_files |>
#      as.vector()

## ----sessionInfo---------------------------------------------------------
#  sessionInfo()