Test GEMmaker

GEMmaker provides example data to quickly show how it works. This data consists of a small set of local files (contained with GEMmaker) and a remote sample from the NCBI’s SRA repository. These samples are small to demonstrate usage for a mixed set of local and remote files. This example assumes you have Singularity installed.


For the examples on this page, Singularity will be used. Singularity will automatically retrieve the GEMmaker Docker images and by default will store them in the work folder that Nextflow creates. However, Nextflow may warn that a cache directory is not set. If you intend to run GEMmaker multipe times, you may wish to designate a permanent cache directory by seting the NXF_SINGULARITY_CACHEDIR prior to running GEMmaker. You can learn more at the nf-core tools page

You can run the example by executing the following command within the GEMmaker directory:

nextflow run systemsgenetics/gemmaker -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>

Replace the text <docker/singularity/podman/shifter/charliecloud/conda/institute> with the execution profile of your choice. For example to test GEMmaker in a Singularity image the command would be.

nextflow run systemsgenetics/gemmaker -profile test,singularity

Results are stored in the results directory. You can find more information about the results in the Use GEMmaker section

About the Demo Test Data

The demo data provided by GEMmaker belongs to the imaginary CORG organism. For the local example, we use a set of 3 artificially made RNA-seq runs. The fictitious CORG organism has a very small “genome” of only 2,336 nucleotides, 3 “chromosomes” and 6 “genes”. The 6 genes are named gene_Alpha, gene_Beta, gene_Zeta, gene_Gamma, gene_Delta, gene_Epsilon.

For the remote data file, GEMmaker automatically downloads a very small RNA-seq file from NCBI. This dataset is from an uncharacterized bacteria, but luckily, CORG shares 3 of the genes with this bacteria so we can use CORG’s reference file. This remote sample was selected becasue it is an unusually small file, making it ideal for the example dataset.