Generic Workflow Template for systemPipeR WMS

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-riboseq 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

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-riboseq.git", mydirname = "sprwf-riboseq")
setwd("sprwf-riboseq")
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 enforcement can be overwritten (not recommended) 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.

Additional Options

To use other param and data repos than the defaults, their URLs 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")

Git CLI Approach

Alternatively, the workflow repos can be cloned with the standard git clone command. Downloading the repos as a Zip file is another option. After this the param and data directories need to be populated with the above get* commands, or by manually copying the corresponding directories from the sprwfcmp-param and sprwfcmp-data repositories.