nf-core/hlatyping

Issues

• No executable found for solver 'cbc'

  #161 opened 8 months ago by DarkoCucin
  5

• No cat_fastq? Sample with multiple run are not handled

  #148 opened 2 years ago by praveenraj2018
  2

• DictReader seems to not be handling utf-encoding properly

  #154 opened 2 years ago by thomasyu888
  3

• Possible error due to accessing files in S3 bucket

  #153 opened 2 years ago by Pharmacogenetecist
  2

• The example sample sheet for running with BAM file input seems incorrect

  #149 opened 2 years ago by jowkar
  5

• adding HLA-VBseq as a new module

  #147 opened 2 years ago by chrstphdm
  1

• adding HLAscan as a new module

  #146 opened 2 years ago by chrstphdm
  1

• Evaluate interest of using an algorithm for combining results

  #145 opened 2 years ago by chrstphdm
  1

• Provide bwa mem / bwa mem2 mode

  #106 opened 4 years ago by apeltzer
  2

• Make the pipeline run with different file sizes

  #108 opened 4 years ago by szymonwieloch
  1

• OptiTypePipeline.py error "Could not retrieve index file"

  #109 opened 2 years ago by ibwoo
  8

• HLA reference: unclear release version

  #29 opened 2 years ago by sven1103
  2

• Improve resource management of pre-filtering step

  #114 opened 2 years ago by apeltzer
  2

• Unclear how to build files for base_index_path

  #111 opened 4 years ago by szymonwieloch
  0

• Pipeline fails when using a relative path for base_index_path

  #110 opened 2 years ago by szymonwieloch
  1

• Add yara indexing to the pipeline

  #112 opened 2 years ago by szymonwieloch
  3

• Add OptiType results to MultiQC

  #105 opened 2 years ago by apeltzer
  3

• aws specific crash with multiqc

  #102 opened 2 years ago by cariaso
  3

• azure specific crash with multiqc

  #130 opened 2 years ago by vsmalladi
  1

• Clean up Tempalte branch

  #107 opened 2 years ago by apeltzer
  2

• Provide design file input

  #104 opened 2 years ago by apeltzer
  2

• Getting unbound variable error in optitype(hlatyping) pipeline: Can someone help me

  #125 opened 2 years ago by varun171
  6

• Cannot find any reads matching: "mypath/sampleID_*.fastq.gz"

  #128 opened 3 years ago by Biojenifer
  1

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

  #126 opened 3 years ago by varun171
  1

• Clean up the temp folder

  #121 opened 4 years ago by joonan30
  2

• DSLv2ify the pipeline

  #115 opened 4 years ago by apeltzer
  2

• HLATYPING: Convert usage docs to JSON schema parameter docs

  #113 opened 4 years ago by apeltzer
  0

• Aggregate results from multiple samples

  #72 opened 4 years ago by gurpreet-bioinfo
  4

• configbuilder: command not found

  #77 opened 4 years ago by pandyark
  3

• Fix input parameter

  #75 opened 4 years ago by christopher-mohr
  1

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

  #70 opened 4 years ago by gurpreet-bioinfo
  7

• parameters missing in docs toc

  #71 opened 4 years ago by ggabernet
  3

• The --index option is ignored

  #76 opened 4 years ago by micknudsen
  10

• 'remap_to_hla' index declaration

  #68 opened 4 years ago by kkyung412
  2

• Erorr running hlatyping with singularity

  #88 opened 4 years ago by nvk747
  2

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

  #57 opened 4 years ago by sven1103
  4

• Plans on class II?

  #67 opened 4 years ago by acrinklaw
  7

• Use RNA/DNA reference genomes correctly.

  #48 opened 4 years ago by apeltzer
  0

• Cannot run HLATyping with user-specific BAM file

  #74 opened 5 years ago by NTNguyen13
  25

• nf-core pipelines should provide structured output information

  #64 opened 5 years ago by sven1103
  2

• Pipeline completed without hla_run_result.tsv file

  #56 opened 6 years ago by giovianco
  2

• Fix configs release...

  #51 opened 6 years ago by apeltzer
  0

• Running with test parameters, how to specify readPaths

  #40 opened 6 years ago by PhilPalmer
  8

• Consider scrape_software_versions

  #36 opened 6 years ago by apeltzer
  0

• Null -- hla reference index

  #37 opened 6 years ago by praveenbas
  5

• Add a DOI on first release

  #16 opened 6 years ago by apeltzer
  1

• HLA result files overwritten

  #30 opened 6 years ago by PeterBailey
  0

• No Container version found

  #17 opened 6 years ago by Rotholandus
  1

• Container image not pulled from shub on profile `singularity`

  #12 opened 6 years ago by sven1103
  11

• HLA typing - mapping of RNAseq fastqs - avoiding RazerS ressource dependencies

  #13 opened 6 years ago by PeterBailey
  2