nf-core/metapep
From metagenomes to epitopes and beyond
An incompatibility advisory with severity high has been
issued for this version of the pipeline.
See the advisory entry for more information.
Launch version 1.0.0 https://github.com/nf-core/metapep See the advisory entry for more information.
Version history
First release of nf-core/metapep
Main functionality:
- Download proteins for input type taxa from Entrez.
- Predict proteins for input type assembly or bins using Prodigal.
- Generate peptides from proteins.
- Split peptide files into chunks for parallel prediction and report stats.
- Predict epitopes for given alleles and peptides using SYFPEITHI, MHCflurry or MHCnuggets.
- Downstream visualizations between conditions (different microbiomes assemblies, bins, taxids or same input class with different weights) given within samplesheet
- Summarize workflow using MultiQC
- Relational datamodel to handle large amounts of data Tables defined within model
- Additional subworkflow to fetch possible model and peptide lengths for the prediction tools