A nextflow wrapper for the automation and parallelisation of the METEOR pipeline and its downstream analysis. Release of the pipeline onto nf-core is under development. Uppmax and Rosalind HPC's are the only tested environments for the pipeline.
-
Load Nextflow according to the "nf-core configuration" (
>=20.07.1
) -
Download the pipeline and test it on the nf-mag minimal dataset of paired end illumina reads by modifying the conf/upprun.config file.
-
Run on the uppmax HPC cluster with a single command:
nextflow run main.nf\
-c configs/institutional/uppmax.config\
-c configs/conf/upprun.config
- INRA
- SciLifeLab
- KCL
- KTH