Run GBRS (https://github.com/churchill-lab/gbrs) on paired-end RNAseq data using Nextflow pipelines.
This is adapted to Sumner cluster (slurm, singularity) and uses the jaxreg.jax.org containers repository, follow the User Guide there to add it to your library.
To test it, install nextflow and run:
nextflow run TheJacksonLaboratory/gbrs_nxf -profile singularity,slurm \
-resume --params-file <parameter_yaml_file>Make sure the input files are in the format: ID_*R{1,2}*.fastq.gz
The parameter file is a yaml formatted file that contains at least the
parameter entries:
fastqR1: [path]
fastqR2: [path]
outputDir: [path]
generation: '[G0-G40]'
sex: [M|F]Plus any other optional parameters, which can be shown by passing the --help
argument i.e. nextflow run TheJacksonLaboratory/gbrs_nxf --help