Testing the setup

If you would like to test the installation of the ARMOR workflow, the repository contains a small example data set. This data set contains paired compressed FASTQ files for four samples from the GSE52778 data set, containing only reads aligning to the first 10M bases of chromosome 1 (in the FASTQ directory). In addition, the directory contains a metadata table with information about the four samples, and a reference directory with two collections of reference files (Gencode v28 and Ensembl v93). The provided config.yaml file is already set up for the example data set and will use conda environments to manage the required software and R.

The design matrix and contrast matrix used in the data analysis edgeR_dge.Rmd and DRIMSeq_dtu.Rmd are created using the R functions stats::model.matrix and limma::makeContrasts based on metadata.txt. The expression to create the design matrix (via design) and the contrast matrix (via contrast) is specified in the config.yaml file. More details about how to create the design and contrast matrix can be found in the help pages of stats::model.matrix and limma::makeContrasts.

You can view the created design and contrast matrix with

snakemake --use-conda checkinputs --cores 1

You can test your conda and R configuration immediately by running the workflow on the example data with

snakemake --use-conda --cores 1

If you have all the software in your path or you want to use a manually created conda environment + system R installation, run the workflow with

snakemake --cores 1

See Managing-software for an explanation of the three different ways to manage the software.

Please refer to the troubleshooting page if you encounter any problems.