## ----style, echo = FALSE, results = 'asis'----------------
BiocStyle::markdown()
options(width=60, max.print=1000)
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")), 
    tidy.opts=list(width.cutoff=60), tidy=TRUE)

## ----setup, echo=FALSE, message=FALSE, warning=FALSE, eval=FALSE----
#  suppressPackageStartupMessages({
#      library(systemPipeR)
#  })

## ----spblast-toplogy, eval=TRUE, warning= FALSE, echo=FALSE, out.width="100%", fig.align = "center", fig.cap= "Topology graph of this workflow template.", warning=FALSE----
knitr::include_graphics("results/plotwf_new.png")

## ----genNew_wf, eval=FALSE--------------------------------
#  systemPipeRdata::genWorkenvir(workflow = "new", mydirname = "new")
#  setwd("new")

## ----create_workflow, message=FALSE, eval=FALSE-----------
#  library(systemPipeR)
#  sal <- SPRproject()
#  sal

## ----load_library, eval=FALSE, spr=TRUE-------------------
#  appendStep(sal) <- LineWise(
#      code = {
#      library(systemPipeR)
#      },
#      step_name = "load_library"
#  )

## ----view_sal, message=FALSE, eval=FALSE------------------
#  sal

## ----export_iris, eval=FALSE, spr=TRUE--------------------
#  appendStep(sal) <- LineWise(code={
#      mapply(
#        FUN = function(x, y) write.csv(x, y),
#        x = split(iris, factor(iris$Species)),
#        y = file.path("results", paste0(names(split(iris, factor(iris$Species))), ".csv"))
#      )
#      },
#    step_name = "export_iris",
#    dependency = "load_library"
#  )

## ----gzip, eval=FALSE, spr=TRUE, spr.dep=TRUE-------------
#  targetspath <- system.file("extdata/cwl/gunzip", "targets_gunzip.txt", package = "systemPipeR")
#  appendStep(sal) <- SYSargsList(
#      targets = targetspath, dir = TRUE,
#      wf_file = "gunzip/workflow_gzip.cwl", input_file = "gunzip/gzip.yml",
#      dir_path = "param/cwl",
#      inputvars = c(FileName = "_FILE_PATH_", SampleName = "_SampleName_"),
#      step_name = "gzip",
#      dependency = "export_iris"
#  )

## ----gunzip, eval=FALSE, spr=TRUE-------------------------
#  appendStep(sal) <- SYSargsList(
#      targets = "gzip", dir = TRUE,
#      wf_file = "gunzip/workflow_gunzip.cwl", input_file = "gunzip/gunzip.yml",
#      dir_path = "param/cwl",
#      inputvars = c(gzip_file = "_FILE_PATH_", SampleName = "_SampleName_"),
#      rm_targets_col = "FileName",
#      step_name = "gunzip",
#      dependency = "gzip"
#  )

## ----stats, eval=FALSE, spr=TRUE--------------------------
#  appendStep(sal) <- LineWise(code={
#      # combine all files into one data frame
#      df <- lapply(getColumn(sal, step="gunzip", 'outfiles'), function(x) read.delim(x, sep=",")[-1])
#      df <- do.call(rbind, df)
#      # calculate mean and sd for each species
#      stats <- data.frame(cbind(mean=apply(df[,1:4], 2, mean), sd=apply(df[,1:4], 2, sd)))
#      stats$species <- rownames(stats)
#      # plot
#      plot <- ggplot2::ggplot(stats, ggplot2::aes(x=species, y=mean, fill=species)) +
#          ggplot2::geom_bar(stat = "identity", color="black", position=ggplot2::position_dodge()) +
#          ggplot2::geom_errorbar(
#              ggplot2::aes(ymin=mean-sd, ymax=mean+sd),
#              width=.2,
#              position=ggplot2::position_dodge(.9)
#          )
#      plot
#      },
#      step_name = "stats",
#      dependency = "gunzip",
#      run_step = "optional"
#  )

## ----sessionInfo, eval=FALSE, spr=TRUE--------------------
#  appendStep(sal) <- LineWise(
#      code = {
#      sessionInfo()
#      },
#      step_name = "sessionInfo",
#      dependency = "stats")

## ----import_run_routine, eval=FALSE-----------------------
#  sal <- SPRproject(overwrite = TRUE) # Avoid 'overwrite=TRUE' in real runs.
#  sal <- importWF(sal, file_path = "new.Rmd") # Imports above steps from new.Rmd.
#  sal <- runWF(sal) # Runs workflow.
#  plotWF(sal) # Plots workflow topology graph
#  sal <- renderReport(sal) # Renders scientific report.
#  sal <- renderLogs(sal) # Renders technical report from log files.

## ----list_tools-------------------------------------------
if(file.exists(file.path(".SPRproject", "SYSargsList.yml"))) {
    local({
        sal <- systemPipeR::SPRproject(resume = TRUE)
        systemPipeR::listCmdTools(sal)
        systemPipeR::listCmdModules(sal)
    })
} else {
    cat(crayon::blue$bold("Tools and modules required by this workflow are:\n"))
    cat(c("gzip", "gunzip"), sep = "\n")
}

## ----report_session_info, eval=TRUE-----------------------
sessionInfo()