epitopeprediction
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nf-core
A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
Version `2.14.1` of [nf-core/tools](https://github.com/nf-core/tools) has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline. Please make sure to...
### Description of the bug Currently the columns **_variant details (genomic)_** and **_variant details (protein)_** are only filled when using snpeff as annotation tool , not VEP. Is there a...
Small release: - Merge template update 2.13.1 - Remove `Channel.view` statement that has accidently sneaked its way into the previous release ## PR checklist - [x] This comment contains a...
### Description of feature The pipeline should also be able to predict putative Neo-epitopes based on structural variants (SV). Currently we only support SNVs and small indels. Predicting Neo-epitopes based...
This adds the option to provide expression values for the peptide prediction and includes the following changes - adapt sample sheet check - handle expression file along channels and add...
It should be a subworkflow that replaces the function [make_predictions_from_peptides](https://github.com/nf-core/epitopeprediction/blob/b0f0d7a5b3cd352e548901e4cc19937c73add465/bin/epaa.py#L1111C5-L1111C35) in epaa.py. That subworkflow takes as input a tsv file containing a column sequence (and additional metadata). Depending on the...
### Description of feature Add syfpeithi as a standalone module in new structure https://github.com/nf-core/epitopeprediction/issues/205
### Description of feature Add netmhcpan and netmhciipan as a standalone module in new structure https://github.com/nf-core/epitopeprediction/issues/205
### Description of feature Add mhcflurry as a standalone module in new structure https://github.com/nf-core/epitopeprediction/issues/205
### Description of feature Add mhcnuggets as a standalone module in new structure #205