R/app-cellRangerAggr.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

###################################################################
# Functional Genomics Center Zurich
# This code is distributed under the terms of the GNU General
# Public License Version 3, June 2007.
# The terms are available here: http://www.gnu.org/licenses/gpl.html
# www.fgcz.ch

EzAppCellRangerAggr <-
  setRefClass("EzAppCellRangerAggr",
    contains = "EzApp",
    methods = list(
      initialize = function() {
        "Initializes the application using its specific defaults."
        runMethod <<- ezMethodCellRangerAggr
        name <<- "EzAppCellRangerAggr"
        appDefaults <<- rbind(normalize = ezFrame(
          Type = "character",
          DefaultValue = "mapped",
          Description = "String specifying how to normalize depth across the input libraries. mapped or none."
        ))
      }
    )
  )

ezMethodCellRangerAggr <- function(input = NA, output = NA, param = NA) {
  ## dataset mode

  aggr_input <- tibble(
    sample_id = input$getNames(),
    molecule_h5 = file.path(
      dirname(input$getFullPaths("Report")), "molecule_info.h5"
    )
  )
  if (any(input$columnHasTag("Factor"))) {
    aggr_input2 <- as_tibble(input$meta[, input$columnHasTag("Factor"), drop = FALSE],
      rownames = "sample_id"
    )
    colnames(aggr_input2) <- str_replace(colnames(aggr_input2), " \\[.*", "")
    aggr_input <- left_join(aggr_input, aggr_input2)
  }

  aggr_input_fn <- tempfile(
    pattern = "aggr_input", tmpdir = getwd(), fileext = ".csv"
  )
  write_csv(aggr_input, file = aggr_input_fn)

  cellRangerFolder <- str_c(param$name, "-cellRanger")
  cmd <- str_c(
    "cellranger aggr", str_c("--id=", cellRangerFolder),
    str_c("--csv=", aggr_input_fn),
    str_c("--normalize=", param$normalize), sep=" "
  )
  ezSystem(cmd)

  file.rename(file.path(cellRangerFolder, "outs"), param$name)
  unlink(cellRangerFolder, recursive = TRUE)

  return("Success")
}