Rules to create a new Workflow Template
How to create a new Workflow Template
SPRthis
package expand usethis package, providing automation to create systemPipeR workflows templates.
Installation
To install SPRthis
using from BiocManager
the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
BiocManager::install("dcassol/SPRthis")
Quick start to using to SPRthis
## Load the package
library(SPRthis)
## create Package
sprthis(wfName="SPRtest", analysis="SPRtest", path=tempdir())
## ✓ Setting active project to '/tmp/RtmpWTh4tB'
## ✓ Creating 'R/'
## ✓ Writing 'DESCRIPTION'
## Package: SPRtest
## Title: SPRtest
## Version: 0.9.0
## Authors@R (parsed):
## * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
## Description: This package provides a pre-configured workflow and reporting
## template for SPRtest.
## License: Artistic-2.0
## URL: https://github.com/systemPipeR/SPRtest
## Imports:
## systemPipeR (>= 1.25.0)
## Suggests:
## BiocStyle,
## knitr,
## rmarkdown
## VignetteBuilder:
## knitr
## biocViews: Infrastructure, ...
## Encoding: UTF-8
## LazyData: true
## Roxygen: list(markdown = TRUE)
## RoxygenNote: 7.1.1
## SystemRequirements: SPRtest can be used to run external command-line
## software, but the corresponding tool needs to be installed on a
## system.
## ✓ Writing 'NAMESPACE'
## ✓ Setting active project to '<no active project>'
## [1] "/tmp/RtmpWTh4tB"
SPRtest/ ├── DESCRIPTION ├── NAMESPACE ├── README.md ├── SPRtest.Rproj ├── .gitignore ├── .Rbuildignore ├── .Rproj.user/ ├── R/ │ ├── functions.R ├── vignettes │ ├── bibtex.bib │ ├── SPRtest.Rmd └── inst ├── rmarkdown │ └── templates │ └── SPRtest │ ├── template.yml │ └── skeleton │ ├── batchtools.slurm.tmpl │ ├── .batchtools.conf.R │ ├── bibtex.bib │ ├── NEWS │ ├── SPRconfig.yml │ ├── skeleton.Rmd │ ├── targetsPE.txt │ ├── data/ │ ├── param/ │ └── results/
Help functions to create the package
Create the webiste for the package with pkgdown
Edit the _pkgdown.yml
file and run:
pkgdown::build_site()
Documentation with roxygen2
roxygen2::roxygenise()
Testing the code with testthat
To test the code, you can run
devtools::test()
Package available to genWorkenvir
Function
After creating the new repository on GitHub systemPipeR Organization, please follow:
- Rules:
- The Workflow Template need to be available under systemPipeR Organization;
- The repository needs to be
public
; - About setting:
Description
: keywords in the description are required: “Workflow Template”;Topics
: we expected “systempiper” and “release” or “development” words on Topics section;
- Branch name: To make simple, please name the branch as “master”.
Check availability of workflow templates
A collection of workflow templates are available, and it is possible to browse the current availability, as follows:
systemPipeRdata::availableWF(github = TRUE)
## $systemPipeRdata
## [1] "chipseq" "new" "riboseq" "rnaseq" "varseq"
##
## $github
## workflow branches version
## 1 systemPipeR/SPchipseq master release
## 2 systemPipeR/SPriboseq master release
## 3 systemPipeR/SPrnaseq cluster, master, singleMachine release
## 4 systemPipeR/SPvarseq master release
## 5 systemPipeR/SPclipseq master devel
## 6 systemPipeR/SPdenovo master devel
## 7 systemPipeR/SPmetatrans master devel
## 8 systemPipeR/SPmethylseq master devel
## 9 systemPipeR/SPmirnaseq master devel
## html description
## 1 https://github.com/systemPipeR/SPchipseq Workflow Template
## 2 https://github.com/systemPipeR/SPriboseq Workflow Template
## 3 https://github.com/systemPipeR/SPrnaseq Workflow Template
## 4 https://github.com/systemPipeR/SPvarseq Workflow Template
## 5 https://github.com/systemPipeR/SPclipseq Workflow Template
## 6 https://github.com/systemPipeR/SPdenovo Workflow Template
## 7 https://github.com/systemPipeR/SPmetatrans Workflow Template
## 8 https://github.com/systemPipeR/SPmethylseq Workflow Template
## 9 https://github.com/systemPipeR/SPmirnaseq Workflow Template
This function returns the list of workflow templates available within the package and systemPipeR Project Organization on GitHub. Each one listed template can be created as described above.
Last modified
2023-10-02
: rebuild no_render (acf0bd05)