nf-core/epitopeprediction issues and pull requests

#230 - Release 2.3.0

Pull Request - State: open - Opened by jonasscheid about 1 year ago - 1 comment

#229 - Prepare release 2.3.0

Pull Request - State: closed - Opened by jonasscheid about 1 year ago - 2 comments

#228 - Merging template 2.12.1

Pull Request - State: closed - Opened by jonasscheid about 1 year ago - 2 comments

#227 - Prevent crash if no transcript is found (in splitted vcf)

Pull Request - State: closed - Opened by jonasscheid about 1 year ago - 1 comment

#226 - Important! Template update for nf-core/tools v2.12

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago

#225 - updating README + show_supported_models fix

Pull Request - State: open - Opened by thomas-davis about 1 year ago - 4 comments

#224 - show_supported_models module not called correctly

Issue - State: open - Opened by jonasscheid about 1 year ago - 1 comment
Labels: bug, good first issue

#223 - Important! Template update for nf-core/tools v2.11.1

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago - 1 comment

#222 - Important! Template update for nf-core/tools v2.11

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago - 1 comment

#221 - Remove GSvar and variant tsv input types

Pull Request - State: closed - Opened by jonasscheid about 1 year ago - 1 comment

#220 - Switch to nf-validation

Pull Request - State: closed - Opened by jonasscheid about 1 year ago - 8 comments

#219 - Fix external tools import container

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 2 comments

#218 - Fix external tools import container

Pull Request - State: closed - Opened by jonasscheid over 1 year ago - 2 comments

#217 - Add syfpeithi module

Issue - State: open - Opened by jonasscheid over 1 year ago
Labels: enhancement

#216 - Add netmhc(ii)pan module

Issue - State: open - Opened by jonasscheid over 1 year ago
Labels: enhancement

#215 - Add mhcflurry module

Issue - State: open - Opened by jonasscheid over 1 year ago
Labels: enhancement

#214 - Add mhcnuggets module

Issue - State: open - Opened by jonasscheid over 1 year ago
Labels: enhancement

#213 - Update epytope and Ensembl reference handling

Pull Request - State: closed - Opened by christopher-mohr over 1 year ago - 1 comment
Labels: enhancement

#212 - Important! Template update for nf-core/tools v2.10

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago

#211 - Allele data can also be used via internet link in sample sheet

Pull Request - State: closed - Opened by alina-bauer over 1 year ago - 4 comments

#210 - New structure of mhc binding subworkflow

Pull Request - State: closed - Opened by alina-bauer over 1 year ago - 1 comment

#209 - Check sample sheet uses Row Checker class

Pull Request - State: closed - Opened by alina-bauer over 1 year ago - 2 comments

#208 - Ensemble archive GRCh38 is out of date (apr2018)

Issue - State: open - Opened by tlitfin over 1 year ago - 6 comments
Labels: bug

#207 - Rewrite and move check_requested_models in input_check subworkflow

Issue - State: open - Opened by jonasscheid over 1 year ago
Labels: enhancement, question

#206 - Check sample sheet doesn't use RowChecker class

Issue - State: open - Opened by jonasscheid over 1 year ago
Labels: enhancement

#205 - Update general structure of MHCbinding subworkflow

Issue - State: open - Opened by alina-bauer over 1 year ago
Labels: enhancement

#203 - Merging template updates 2 9

Pull Request - State: closed - Opened by christopher-mohr over 1 year ago - 1 comment

#202 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago

#201 - Proteome CLI flags of epaa and nextflow differ

Issue - State: open - Opened by jonasscheid over 1 year ago - 2 comments
Labels: bug

#200 - change to epytope 3.3.1 version and new multi container for peptide prediction

Pull Request - State: closed - Opened by jonasscheid almost 2 years ago - 21 comments

#199 - Important! Template update for nf-core/tools v2.8

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 1 comment

#198 - Release 2.2.1 bugfix

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 1 comment

#197 - bump version to 2.2.1

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 1 comment

#196 - Fix external tools prediction

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 2 comments

#195 - Version 2.2.0 does not produce any predictions anymore for netmhcpan class 1

Issue - State: closed - Opened by steffenlem almost 2 years ago - 3 comments
Labels: bug

#194 - Address review comments

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 3 comments

#193 - Use nf-core modules

Issue - State: open - Opened by ggabernet almost 2 years ago
Labels: enhancement

#192 - Bump versions 2.2.0

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 1 comment

#191 - Prepare release 2.2.0

Pull Request - State: closed - Opened by ggabernet almost 2 years ago - 4 comments

#189 - Merge template update

Pull Request - State: closed - Opened by christopher-mohr about 2 years ago - 3 comments

#188 - Important! Template update for nf-core/tools v2.7.2

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago

#187 - Merge template 2.7.1

Pull Request - State: closed - Opened by christopher-mohr about 2 years ago - 1 comment

#186 - Logging to stdout and better errors

Pull Request - State: closed - Opened by ggabernet about 2 years ago - 1 comment

#185 - Important! Template update for nf-core/tools v2.7.1

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago

#184 - Fix external tool version

Pull Request - State: closed - Opened by christopher-mohr about 2 years ago - 1 comment

#183 - Issue with the process: EXTERNAL_TOOLS_IMPORT

Issue - State: closed - Opened by marissaDubbelaar about 2 years ago - 3 comments
Labels: bug

#182 - Update GRCh38 biomart archive

Pull Request - State: closed - Opened by christopher-mohr about 2 years ago - 1 comment

#181 - Add Manta support for structural variant prediction

Issue - State: open - Opened by jonasscheid over 2 years ago - 2 comments
Labels: enhancement

#180 - Add vep support

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 3 comments

#179 - Important! Template update for nf-core/tools v2.6

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago

#178 - Update nf-core modules

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 1 comment

#177 - Merge template update 2.5.1

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 2 comments

#176 - Important! Template update for nf-core/tools v2.5.1

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago

#175 - Important! Template update for nf-core/tools v2.5

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 2 comments

#174 - Add rnaseq input

Pull Request - State: open - Opened by christopher-mohr over 2 years ago - 2 comments
Labels: do not merge

#173 - bump version

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 1 comment

#172 - Add support for VEP annotated files

Issue - State: closed - Opened by christopher-mohr over 2 years ago
Labels: enhancement

#171 - release 2.1.0

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 1 comment

#170 - Add general binder column

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 1 comment

#169 - Update modules

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 3 comments

#168 - Add functionality for prediction with multiple classes in one run

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 1 comment

#167 - Fix bug that results in empty prediction results

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 1 comment

#166 - Increment support of netmhc tools

Pull Request - State: closed - Opened by jonasscheid over 2 years ago - 1 comment

#165 - Add tools to full size test

Pull Request - State: closed - Opened by ggabernet over 2 years ago - 2 comments

#164 - Switch to epytope

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 1 comment

#163 - Add threshold to report

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 1 comment

#162 - Update to epytope 3.1.0

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 1 comment

#161 - Add threshold function for rank and set affinity as optional

Pull Request - State: closed - Opened by jonasscheid over 2 years ago - 2 comments

#160 - Extend binding threshold with rank metric

Issue - State: closed - Opened by jonasscheid over 2 years ago
Labels: enhancement

#159 - Fix execution for multiple samples of same input type

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 4 comments

#158 - update trigger for nonfree CI tests

Pull Request - State: closed - Opened by ggabernet over 2 years ago - 2 comments

#157 - add config for external prediction tools

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 1 comment

#156 - Add documentation

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 1 comment

#155 - Add functionality for splitting input VCF files by variants

Pull Request - State: closed - Opened by christopher-mohr over 2 years ago - 1 comment
Labels: enhancement

#154 - Switch to epytope

Pull Request - State: closed - Opened by jonasscheid over 2 years ago - 1 comment

#153 - Important! Template update for nf-core/tools v2.4

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 1 comment

#152 - Template merge for last updates

Pull Request - State: closed - Opened by christopher-mohr almost 3 years ago - 2 comments

#151 - Important! Template update for nf-core/tools v2.3.2

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago

#150 - Important! Template update for nf-core/tools v2.3.1

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 1 comment

#149 - More adaptations for eptyope

Pull Request - State: closed - Opened by christopher-mohr almost 3 years ago - 3 comments

#148 - Epytope switch in process peptide_prediction

Pull Request - State: closed - Opened by jonasscheid almost 3 years ago - 2 comments

#147 - Important! Template update for nf-core/tools v2.3

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 1 comment

#146 - KeyError: 'Transcript ID'

Issue - State: closed - Opened by marissaDubbelaar almost 3 years ago - 2 comments
Labels: bug, status: awaiting feedback

#145 - Support gzipped variant input

Pull Request - State: closed - Opened by christopher-mohr almost 3 years ago - 1 comment

#144 - Check FORMAT entries in VCF parser

Pull Request - State: closed - Opened by christopher-mohr almost 3 years ago - 1 comment

#143 - Splitting a zipped vcf.gz file

Issue - State: closed - Opened by marissaDubbelaar almost 3 years ago
Labels: bug

#142 - No attribute 'MIN_DP'

Issue - State: closed - Opened by marissaDubbelaar almost 3 years ago - 1 comment
Labels: bug

#141 - Missing output information in neoepitopeprediction snvs and indels

Issue - State: closed - Opened by jonasscheid almost 3 years ago - 2 comments
Labels: bug, status: awaiting feedback

#140 - Neoepitopeprediction is too memory demanding

Issue - State: closed - Opened by jonasscheid almost 3 years ago - 1 comment
Labels: enhancement

#139 - Fix linting and samplesheet check

Pull Request - State: closed - Opened by christopher-mohr about 3 years ago - 1 comment

#138 - Add lint config

Pull Request - State: closed - Opened by christopher-mohr about 3 years ago - 2 comments

#137 - Fix markdown linting

Pull Request - State: closed - Opened by christopher-mohr about 3 years ago - 1 comment

#136 - Neoepitopeprediction crashes when a variant has annotated metadata, which is not available for others

Issue - State: closed - Opened by jonasscheid about 3 years ago
Labels: bug

#135 - Fix unique variant annotation field handling #136

Pull Request - State: closed - Opened by jonasscheid about 3 years ago - 3 comments

#134 - Add RNAseq table as input

Issue - State: open - Opened by ggabernet about 3 years ago - 1 comment
Labels: enhancement

#133 - Change result folder structure

Pull Request - State: closed - Opened by christopher-mohr about 3 years ago - 4 comments

#132 - Bump version to 2.1.0dev

Pull Request - State: closed - Opened by christopher-mohr about 3 years ago - 2 comments

#131 - Reorganize result folder structure

Issue - State: closed - Opened by christopher-mohr about 3 years ago
Labels: enhancement

#130 - Use Epytope instead of Fred2 once the release is available

Issue - State: closed - Opened by ggabernet about 3 years ago
Labels: enhancement

#129 - remove fastqc module

Pull Request - State: closed - Opened by ggabernet about 3 years ago

GitHub / nf-core/epitopeprediction issues and pull requests