## ----style, echo = FALSE, results = 'asis'--------------------------------------------------------
BiocStyle::markdown()
options(width=100, max.print=1000)
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))

## ----setup, echo=FALSE, messages=FALSE, warnings=FALSE--------------------------------------------
suppressPackageStartupMessages({
    library(systemPipeR)
    library(systemPipeRdata)
    library(BiocGenerics)
})

## ----load_systemPipeRdata, eval=TRUE--------------------------------------------------------------
library("systemPipeRdata") # Loads the package

## ----documentation_systemPipeRdata, eval=FALSE----------------------------------------------------
#  library(help="systemPipeRdata") # Lists package info
#  vignette("systemPipeRdata") # Opens vignette

## ----generate_workenvir, eval=FALSE---------------------------------------------------------------
#  genWorkenvir(workflow="varseq", mydirname=NULL)
#  setwd("varseq")

## ----workflow_template_structure, eval=FALSE------------------------------------------------------
#  workflow_name/            # *.Rnw/*.Rmd scripts and targets file
#                  param/    # parameter files for command-line software
#                  data/     # inputs e.g. FASTQ, reference, annotations
#                  results/  # analysis result files

## ----load_systemPipeR, eval=TRUE------------------------------------------------------------------
library("systemPipeR") # Loads systemPipeR which needs to be installed via BiocManager::install() from Bioconductor

## ----documentation_systemPipeR, eval=FALSE--------------------------------------------------------
#  vignette("systemPipeR", package = "systemPipeR")

## ----return_samplepaths, eval=TRUE----------------------------------------------------------------
pathList()

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