In tgirke/systemPipeR: systemPipeR: workflow management and report generation environment

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

```r
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)

Introduction

This is a test template.

Samples and environment settings

Required packages and resources

The systemPipeR package needs to be loaded to perform the analysis steps shown in this report [@H_Backman2016-bt].

appendStep(sal) <- LineWise(code={
  library(systemPipeR)
  },
  step_name = "load_systempiper", 
  dependency = NA)

SYSargsList example

targetspath <- system.file("extdata", "targetsPE.txt", package = "systemPipeR")
appendStep(sal) <- SYSargsList(step_name = "quality",
                               targets=targetspath, 
                   wf_file = "trimmomatic/workflow_trimmomatic-pe.cwl", 
                   input_file = "trimmomatic/trimmomatic-pe.yml",
                   dir_path=system.file("extdata/cwl", package = "systemPipeR"),
                   inputvars=c(FileName1="_FASTQ_PATH1_", FileName2="_FASTQ_PATH2_", SampleName="_SampleName_"))

appendStep(sal) <- SYSargsList(step_name = "index",
                               dir = FALSE,
                               targets=NULL, 
                               wf_file = "hisat2/workflow_hisat2-index.cwl",
                               input_file="hisat2/hisat2-index.yml",
                               dir_path=system.file("extdata/cwl", package = "systemPipeR"), 
                               dependency = "quality")

appendStep(sal) <- SYSargsList(targets="quality",
                               dir=TRUE, 
                               wf_file = "workflow-hisat2/workflow_hisat2-pe.cwl",
                               input_file="workflow-hisat2/workflow_hisat2-pe.yml",
                               dir_path=system.file("extdata/cwl", package = "systemPipeR"),
                               inputvars=c(trimmomatic_1_paired="_FASTQ_PATH1_",
                                           trimmomatic_2_paired="_FASTQ_PATH2_", SampleName="_SampleName_"),
                               rm_targets_col = c("FileName1", "FileName2"),
                               dependency = c("quality", "index"))

Version Information

appendStep(sal) <- LineWise(code={
  sessionInfo()
  },
  step_name = "sessionInfo", 
  dependency = "Mapping")

Funding

This project was supported by funds from the National Institutes of Health (NIH).

References

tgirke/systemPipeR documentation built on March 27, 2024, 11:31 p.m.