NEWS

systemPipeR 1.22

With the upgrades provided in this release, systemPipeR has become a much more generic data analysis workflow environment that is no longer limited to analyzing just NGS data. Now it can be efficiently used for data analysis tasks in many omics areas, including genomics, proteomics, metabolomics and drug discovery.
A workflow control class (SYSargsList) has been added allowing users to manage multiple-step workflows from a single container. This way one can select and execute multiple workflow steps with standard R subsetting syntax, e.g. runWF[1:3].
Various improvements have been added to systemPipeR’s new command-line interface including the recently introduced SYSargs2 class that supports the Common Workflow Language (CWL).
Utilities have been added to visualize workflow designs and topologies with different graphical layouts.
Improvements have been added to monitor the run status of workflows as well as better tracking of warning and error messages. This includes the generation of both scientific and technical status reports.

systemPipeR is an R/Bioconductor package for building and running automated analysis workflows for a wide range of next generation sequence (NGS) applications. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure.
The most important enhancements in the upcoming release of the package are outlined below.

Added new end-to-end workflows for 3 additional NGS application areas: - Ribo-Seq and polyRibo-Seq - ChIP-Seq - VAR-Seq The previous version of systemPipeR included only a complete workflow for RNA-Seq.
Added the data package 'systemPipeRdata' to generate systemPipeR workflow environments with a single command (genWorkenvir) containing all parameter files and sample data required to quickly test and run workflows. This change will also allow evaluation of much more code examples in the vignettes during the package build/test process than this was possible in the past.
About 20 new functions have been added to the package. Some examples are: - Read pre-processor function with support for SE and PE reads - Parallelization option of detailed FASTQ quality reports - Read distribution plots across all features available in a genome annotation (see ?featuretypeCounts) - Visualization of coverage trends along transcripts summarized for any number of transcripts (see ?featureCoverage) - Functionalities to predict uORFs/sORFs and to use them for expression profiling - Differential expression/binding analysis includes now DESeq2 as well as edgeR
Added param templates for additional command-line software including, but not limited to: BWA-MEM, GATK, BCFtools, MACS2
Adoption of R Markdown for main vignette. Future plans are to provide for all workflows the report templates in both formats: Latex/PDF and R_Markdown/HTML.

Simplified design of complex analysis workflows. Workflows can now include any number or combination of R and/or command-line steps
Improvements to workflow automation and parallelization on single machines and computer clusters. This also includes now many additional parallelization examples in the workflow vignettes.