nf-core/metapep: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.0.0 - nf-core/metapep "Golden Megalodon" - [2024-11-22]

First release of nf-core/metapep, based on nf-core standards and nf-core/tools template version 1.14.1.

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
- binding affinities
- entity binding ratios
Summarize workflow using MultiQC
Relational datamodel to handle large amounts of data Tables defined within model:
- alleles.tsv
- condition_alleles.tsv
- conditions.tsv
- entities_proteins.tsv
- entities.tsv
- microbiomes_entities.no_weights.tsv
- microbiome_entities.nucl.tsv
- microbiomes_entities.tsv
- microbiomes.tsv
- preptides.tsv.gz
- predictions.tsv.gz
- proteins_peptides.tsv
- proteins.tsv.gz
- stats.txt
Additional subworkflow to fetch possible model and peptide lengths for the prediction tools