inst/app/data/example_wf.md

In systemPipeShiny: systemPipeShiny: An Interactive Framework for Workflow Management and Visualization

title: "Title" author: "Author: Daniela Cassol ([e-mail]) and Thomas Girke ([e-mail])" date: "Last update: r format(Sys.time(), '%d %B, %Y')" output: BiocStyle::html_document: toc_float: true code_folding: show BiocStyle::pdf_document: default package: systemPipeR vignette: | %\VignetteIndexEntry{RIBO-Seq Workflow Template} %\VignetteEncoding{UTF-8} %\VignetteEngine{knitr::rmarkdown} fontsize: 14pt bibliography: bibtex.bib

```{css, echo=FALSE} pre code { white-space: pre !important; overflow-x: scroll !important; word-break: keep-all !important; word-wrap: initial !important; }

```{r 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)

```{r setup, echo=FALSE, message=FALSE, warning=FALSE, eval=FALSE} suppressPackageStartupMessages({ library(systemPipeR) })

# Introduction

## Load packages and sample data

The `systemPipeR` package needs to be loaded to perform the analysis 
steps shown in this report [@Girke2014-oy]. The package allows users
to run the entire analysis workflow interactively or with a single command 
while also generating the corresponding analysis report. For details
see `systemPipeR's` main [vignette](http://www.bioconductor.org/packages/devel/bioc/vignettes/systemPipeR/inst/doc/systemPipeR.html).

```{r load_systempiper, eval=TRUE, message=FALSE}
library(systemPipeR)

Experiment definition provided by targets file

The targets file defines all FASTQ files and sample comparisons of the analysis workflow.

```{r load_targets, eval=TRUE} targetspath <- system.file("extdata", "targets.txt", package="systemPipeR") targets <- read.delim(targetspath, comment.char = "#")[,1:4] targets

# Version Information

```{r sessionInfo}
sessionInfo()

Funding

References

systemPipeShiny documentation built on March 16, 2021, 6:01 p.m.