The DGE pipeline is already installed in myriad. You just need to load it and start using it:
module load blic-modules
module load nextflow_dge
nextflow_dge --inputdir results_rnaseq --metadata metadata.txt --outdir results_DGE By default, the pipeline runs with the legion configuration profile conf/legion.config if you submit it from legion, and with the myriad config
conf/myriad.config if you send the job from myriad.
The 'standard' configuration (using the local executor) is not enabled.
You'll need to install
- nextflow, eg via bioconda or https://www.nextflow.io/index.html
- the R packages mentioned in bin/run_deseq2.R