nf-core/hlatyping issues and pull requests

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

Pull Request - State: open - Opened by nf-core-bot 9 months ago

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

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

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

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

#154 - DictReader seems to not be handling utf-encoding properly

Issue - State: open - Opened by thomasyu888 about 1 year ago - 3 comments
Labels: bug

#153 - Possible error due to accessing files in S3 bucket

Issue - State: closed - Opened by Pharmacogenetecist over 1 year ago - 2 comments
Labels: bug

#152 - Merge template updates

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

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

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

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

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

#149 - The example sample sheet for running with BAM file input seems incorrect

Issue - State: closed - Opened by jowkar over 1 year ago - 5 comments
Labels: bug

#148 - No cat_fastq? Sample with multiple run are not handled

Issue - State: open - Opened by praveenraj2018 over 1 year ago - 1 comment
Labels: enhancement

#147 - adding HLA-VBseq as a new module

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

#146 - adding HLAscan as a new module

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

#145 - Evaluate interest of using an algorithm for combining results

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

#144 - Release 2.0.0

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

#143 - Bump version to 2.0.0

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

#142 - Fix lint warnings

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

#141 - Add OptiType results to MultiQC

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

#140 - Port pipeline to DSL2

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

#132 - Resolving high memory usage by Yara mapper

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

#131 - Make plots folder optional if empty

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

#130 - azure specific crash with multiqc

Issue - State: closed - Opened by vsmalladi over 2 years ago - 1 comment
Labels: bug

#129 - Important! Template update for nf-core/tools v2.2

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

#128 - Cannot find any reads matching: "mypath/sampleID_*.fastq.gz"

Issue - State: closed - Opened by Biojenifer over 2 years ago - 1 comment

#127 - Important! Template update for nf-core/tools v2.1

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

#126 - Markduplicate in Sarek pipeline is not completing (running for 4 hours) in spark cluster..does anyone know about this..

Issue - State: closed - Opened by varun171 almost 3 years ago - 1 comment

#125 - Getting unbound variable error in optitype(hlatyping) pipeline: Can someone help me

Issue - State: closed - Opened by varun171 almost 3 years ago - 6 comments

#124 - Important! Template update for nf-core/tools v2.0.1

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

#123 - Important! Template update for nf-core/tools v2.0

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

#122 - Important! Template update for nf-core/tools v1.14

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

#121 - Clean up the temp folder

Issue - State: closed - Opened by joonan30 about 3 years ago - 2 comments

#120 - Remove social preview image to use GitHub OpenGraph

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

#119 - Important! Template update for nf-core/tools v1.13.2

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

#118 - Fixed json schema + docs

Pull Request - State: closed - Opened by apeltzer over 3 years ago

#117 - Important! Template update for nf-core/tools v1.13.1

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

#116 - Important! Template update for nf-core/tools v1.13

Pull Request - State: closed - Opened by ewels over 3 years ago - 1 comment

#115 - DSLv2ify the pipeline

Issue - State: closed - Opened by apeltzer over 3 years ago - 2 comments

#114 - Improve resource management of pre-filtering step

Issue - State: closed - Opened by apeltzer over 3 years ago - 2 comments

#113 - HLATYPING: Convert usage docs to JSON schema parameter docs

Issue - State: closed - Opened by apeltzer over 3 years ago

#112 - Add yara indexing to the pipeline

Issue - State: closed - Opened by szymonwieloch over 3 years ago - 3 comments
Labels: enhancement

#111 - Unclear how to build files for base_index_path

Issue - State: open - Opened by szymonwieloch over 3 years ago
Labels: enhancement

#110 - Pipeline fails when using a relative path for base_index_path

Issue - State: closed - Opened by szymonwieloch over 3 years ago - 1 comment
Labels: bug

#109 - OptiTypePipeline.py error "Could not retrieve index file"

Issue - State: closed - Opened by ibwoo over 3 years ago - 8 comments

#108 - Make the pipeline run with different file sizes

Issue - State: open - Opened by szymonwieloch over 3 years ago - 1 comment
Labels: enhancement

#107 - Clean up Tempalte branch

Issue - State: closed - Opened by apeltzer over 3 years ago - 2 comments
Labels: enhancement

#106 - Provide bwa mem / bwa mem2 mode

Issue - State: open - Opened by apeltzer over 3 years ago - 2 comments
Labels: enhancement

#105 - Add OptiType results to MultiQC

Issue - State: closed - Opened by apeltzer over 3 years ago - 3 comments
Labels: enhancement

#104 - Provide design file input

Issue - State: closed - Opened by apeltzer over 3 years ago - 2 comments
Labels: enhancement

#103 - Important! Template update for nf-core/tools v1.12.1

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

#102 - aws specific crash with multiqc

Issue - State: closed - Opened by cariaso almost 4 years ago - 3 comments
Labels: bug

#101 - Update README.md

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

#100 - Bump to next dev version

Pull Request - State: closed - Opened by christopher-mohr almost 4 years ago

#99 - updating dev branch after release

Pull Request - State: closed - Opened by ggabernet almost 4 years ago - 1 comment

#98 - Use all-version DOI and add DOI badge

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

#97 - Fix changelog for release 1.2.0

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

#96 - Release 1.2.0

Pull Request - State: closed - Opened by christopher-mohr almost 4 years ago - 9 comments

#95 - Release/1.2.0

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

#94 - Prepare release 1.2.0

Pull Request - State: closed - Opened by christopher-mohr almost 4 years ago

#93 - Minor changes to README and help message

Pull Request - State: closed - Opened by christopher-mohr almost 4 years ago

#92 - Fix index seq type for rna and correct parameter summary

Pull Request - State: closed - Opened by christopher-mohr almost 4 years ago

#91 - Improve schema, remove prefix parameter

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

#90 - Merging template updates

Pull Request - State: closed - Opened by christopher-mohr almost 4 years ago - 1 comment

#89 - Important! Template update for nf-core/tools v1.10.2

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

#88 - Erorr running hlatyping with singularity

Issue - State: closed - Opened by nvk747 almost 4 years ago - 2 comments

#87 - Update Dockerfile

Pull Request - State: closed - Opened by christopher-mohr almost 4 years ago - 1 comment

#86 - Specify python version

Pull Request - State: closed - Opened by christopher-mohr almost 4 years ago - 1 comment

#85 - Fixes to main.nf and usage.md

Pull Request - State: closed - Opened by nvk747 almost 4 years ago - 2 comments

#84 - Fix the input paramater and missing parameters in the doc

Pull Request - State: closed - Opened by nvk747 almost 4 years ago - 4 comments

#83 - Update container

Pull Request - State: closed - Opened by christopher-mohr almost 4 years ago

#82 - Merge template updates

Pull Request - State: closed - Opened by christopher-mohr almost 4 years ago - 7 comments

#81 - Template update for nf-core/tools version 1.9

Pull Request - State: closed - Opened by christopher-mohr almost 4 years ago

#80 - Add manifest.author variable for sync

Pull Request - State: closed - Opened by christopher-mohr almost 4 years ago

#79 - Patch invalid input index def

Pull Request - State: closed - Opened by pditommaso about 4 years ago - 1 comment

#78 - Add GitHub actions instead of Travis CI

Pull Request - State: closed - Opened by ggabernet about 4 years ago

#77 - configbuilder: command not found

Issue - State: closed - Opened by pandyark about 4 years ago - 3 comments
Labels: good first issue

#76 - The --index option is ignored

Issue - State: closed - Opened by micknudsen about 4 years ago - 10 comments
Labels: bug, good first issue

#75 - Fix input parameter

Issue - State: closed - Opened by christopher-mohr over 4 years ago - 1 comment
Labels: bug, good first issue

#74 - Cannot run HLATyping with user-specific BAM file

Issue - State: closed - Opened by NTNguyen13 over 4 years ago - 25 comments

#73 - Add social preview image

Pull Request - State: closed - Opened by maxulysse over 4 years ago

#72 - Aggregate results from multiple samples

Issue - State: closed - Opened by gurpreet-bioinfo over 4 years ago - 4 comments
Labels: enhancement

#71 - parameters missing in docs toc

Issue - State: closed - Opened by ggabernet over 4 years ago - 3 comments
Labels: good first issue

#70 - Remove --genome and igenomes config from this pipeline as it is not used

Issue - State: closed - Opened by gurpreet-bioinfo over 4 years ago - 7 comments
Labels: enhancement

#69 - Stand alone parameters schema

Pull Request - State: closed - Opened by ewels over 4 years ago - 4 comments

#68 - 'remap_to_hla' index declaration

Issue - State: closed - Opened by kkyung412 over 4 years ago - 2 comments
Labels: bug

#67 - Plans on class II?

Issue - State: closed - Opened by acrinklaw over 4 years ago - 7 comments
Labels: question, upstream

#66 - Mini Patch Branch Test

Pull Request - State: closed - Opened by apeltzer almost 5 years ago

#65 - Add example citation file format

Pull Request - State: closed - Opened by sven1103 almost 5 years ago - 12 comments

#64 - nf-core pipelines should provide structured output information

Issue - State: closed - Opened by sven1103 almost 5 years ago - 2 comments

#63 - PR for 1.1.5 Bugfix Release

Pull Request - State: closed - Opened by apeltzer about 5 years ago

#62 - Fix for multiqc local executor

Pull Request - State: closed - Opened by apeltzer about 5 years ago

#61 - move boilerplate functions to separate lib

Pull Request - State: closed - Opened by phue about 5 years ago - 5 comments
Labels: help wanted, WIP

#60 - Important pipeline nf-core update! (version 1.6)

Pull Request - State: closed - Opened by nf-core-bot about 5 years ago

#59 - Parse parameters.json and use it in the help message

Pull Request - State: closed - Opened by sven1103 about 5 years ago - 8 comments
Labels: WIP

#57 - Parse parameters.settings.json and display params with description in --help

Issue - State: closed - Opened by sven1103 about 5 years ago - 4 comments

GitHub / nf-core/hlatyping issues and pull requests