nf-core/oncoanalyser

Issues

• Reintroduce MultiQC for workflow and analysis summary

  #81 opened 8 months ago by scwatts
  0

• JSON schema: Oncoanalyser

  #165 opened 12 days ago by jen-reeve
  0

• Use pbzip2/pigz for asset decompression

  #135 opened a month ago by brainstorm
  4

• Nf-core spring cleaning 2025: Cosmetics

  #164 opened 23 days ago by jonasscheid
  1

• Pre-index and store BWA testing indices?

  #162 opened 25 days ago by brainstorm
  5

• Align workflows and tools with WiGiTS v6.0

  #119 opened a month ago by scwatts
  0

• Late crash due to yaml parsing issue

  #138 opened a month ago by ajw2329
  6

• Drive reference data and resource file data staging through CLI option

  #131 opened 2 months ago by scwatts
  1

• ERROR::INVALID_FLAG_NOT_PRIM_ALIGNMENT

  #137 opened a month ago by zhaowsong
  5

• Sage `this.mRefContext is null` error

  #133 opened a month ago by silkrp
  5

• Add WISP purity estimation workflow

  #147 opened a month ago by scwatts
  0

• Add panel resource creation workflow

  #146 opened a month ago by scwatts
  0

• Update documentation for WiGiTS v6.0 alignment

  #145 opened a month ago by scwatts
  0

• Implement CIDER

  #144 opened a month ago by scwatts
  0

• Implement PEACH

  #143 opened a month ago by scwatts
  0

• Implement TEAL

  #142 opened a month ago by scwatts
  0

• Support ARM64/AArch64 architecture

  #139 opened a month ago by scwatts
  0

• Add `cancer_type` parameter

  #121 opened a month ago by bounlu
  4

• Staging foreign file reuse across re-runs?

  #136 opened a month ago by brainstorm
  1

• Copy number scatter plots

  #130 opened 2 months ago by Indianhedgehog
  1

• Markdup doesn't accept unpaired reads aligned with minimap2

  #55 opened 9 months ago by charlenelawdes
  5

• cannot locate the log file to figure out the problem.

  #124 opened 3 months ago by Indianhedgehog
  4

• use nf-core on an HPC with internet access

  #114 opened 4 months ago by Donbbit
  4

• Add fusion breakpoints to the `orange` output

  #122 opened 4 months ago by bounlu
  1

• Improve input validation for FASTQ

  #91 opened 7 months ago by scwatts
  1

• Migrate from nf-validation to nf-schema

  #51 opened 4 months ago by scwatts
  1

• Add `vCHORD` to oncoanalyser for HRD detection in targeted mode

  #118 opened 4 months ago by bounlu
  1

• Too low resource requirements and too high heap memory causes processes to go OOM

  #106 opened 4 months ago by mvanniekerkHartwig
  0

• Using oncoanalyser for whole exome sequencing data

  #109 opened 4 months ago by anshupas
  3

• Add option for Sambamba tmp directory

  #112 opened 4 months ago by adbeggs
  1

• Make `circos` plots optional in the `orange` report

  #113 opened 4 months ago by bounlu
  1

• `Rscript` error when running `PURPLE`

  #100 opened 5 months ago by bounlu
  3

• Markdups process marks aligner output as markdups output incorrectly

  #104 opened 5 months ago by mvanniekerkHartwig
  6

• `samplesheet` format is not recognised

  #65 opened 8 months ago by bounlu
  8

• Add support for custom targeted panel

  #66 opened 7 months ago by bounlu
  4

• `markdups` fails with `Range [0, -1) out of bounds` error

  #99 opened 7 months ago by bounlu
  5

• Eliminate bottlenecking of markdups

  #74 opened 7 months ago by SPPearce
  3

• Compatibility of IonTorrent BAM Files for HRD Analysis with nf-core/oncoanalyser

  #92 opened 7 months ago by Sadiki-Noureddine
  1

• Missing type string in one part of nextflow_schema.json

  #93 opened 7 months ago by scoughlan2
  0

• invalid file type: 'fastq'

  #89 opened 8 months ago by jkneppers
  1

• Setting targeted mode without a panel gives an error message containing null

  #77 opened 8 months ago by SPPearce
  1

• Add documentation describing workflow design choices

  #84 opened 8 months ago by scwatts
  0

• Implement basic sequence and alignment QC reporting

  #83 opened 8 months ago by scwatts
  0

• Determine whether certain Groovy syntax should be removed

  #82 opened 8 months ago by scwatts
  0

• Determine future feasibility of switch to nf-core bump-version

  #79 opened 8 months ago by scwatts
  0

• Add reference data to iGenomes

  #80 opened 8 months ago by scwatts
  0

• Shrink reference data to support execution on GHA runners

  #71 opened 8 months ago by FriederikeHanssen
  1

• UMI support in WGTS mode

  #73 opened 8 months ago by SPPearce
  1

• Gene fusion detection

  #63 opened 9 months ago by bounlu
  3

• isofox_read_length does not have a 'type' attribute

  #60 opened 10 months ago by alexiswl
  0