Overview

This is a versioned workflow template for conducting data analyses with the systemPipeR Workflow Management System (WMS). It ensures consistency through centrally maintained param and data packs, which are defined in manifest.yml and downloaded and installed during the setup process.

Detailed information about this specific sprwf-new workflow is available here.

Note: The data pack includes sample data useful for testing certain workflows. Users who do not require this sample data can skip the download step under the getData_gh section below.

Documentation

To design, set up, and run workflows using systemPipeR, please consult:

• systemPipeR Manual
• systemPipeRdata Manual

👉 A complete list of workflow templates and project information is available at systempipe.org.

Quick Start (Recommended)

The following will:

• Clone the workflow using gert internally, which eliminates the need to install the Git CLI
• Enforce minimum package versions
• Install the exact tagged param/ and data/ releases
• Create a reproducible local workflow environment

library(systemPipeRdata)
genWorkenvir_gh(url = "https://github.com/systemPipeR/sprwf-new.git", mydirname = "sprwf-new")
setwd("sprwf-new")
getParam_gh()
getData_gh() # omit if sample data is not needed

Note: param/ and data/ directories are protected by default. If they already exist, they are backed up before new files are installed. See ?getParam_gh and ?getData_gh for overwrite options.

The version dependencies are defined in manifest.yml:

The version enforcement (not recommended) can be overwritten via the force_min_version argument:

genWorkenvir_gh(..., force_min_version = TRUE)

For more information, consult the help pages: ?genWorkenvir_gh, ?getParam_gh, and ?getData_gh.

Advanced Setup Options

The URLs of the param and data repos can be provided under the corresponding *_repos arguments.

getParam_gh(param_repo = "https://github.com/systemPipeR/sprwfcmp-param")
getData_gh(data_repo  = "https://github.com/systemPipeR/sprwfcmp-data")

Command-line Option

Alternatively, the workflow repos can be cloned with the standard git clone command. This requires the install of the Git CLI. The <download_link> is located under the green "Code" button on the top right of the repository, with the HTTPS option generally being the most straightforward for most users. Downloading the repos a zip file is another option.

From the command-line:

git clone <download_link>

After this the param and data directories need to be populated as shown above, or manually by copying the corresponding directories of the sprwfcmp-param and sprwfcmp-data repos into the workflow repository.