epi2me-labs/wf-artic

Issues

• Request to implement a Sunburst plot in the wf-artic report like the wf-metagenomics report

  #113 opened a month ago by mgurbano
  0

• EPI2ME Labs Pangolin does not appear to Update Pangolin when checking "Update Data"

  #112 opened a month ago by mgurbano
  5

• Adding support for dna_r10.4.1_e8.2_400bps_sup@v4.2.0

  #95 opened a year ago by llk578496
  6

• Invalid output definition when I try to run test data

  #111 opened 5 months ago by MauriAndresMU1313
  2

• Error updating Pangolin

  #96 opened 8 months ago by alexahess
  8

• Nextclade version hardcoded

  #110 opened 5 months ago by ammaraziz
  1

• Medaka unable to download model

  #104 opened 5 months ago by ammaraziz
  3

• Nextclade v2 no longer maintained

  #107 opened 8 months ago by ammaraziz
  8

• Missing barcodes from sample input break the pipeline

  #89 opened 8 months ago by ammaraziz
  3

• Error with initial --help command

  #108 opened 9 months ago by kiranpatil222
  1

• ERROR ~ Error executing process > 'pipeline:report' when sample names are numbers only

  #101 opened a year ago by rrdavis77
  5

• No nextclade.tsv output

  #102 opened a year ago by rgn3210
  0

• Readme command is wrong for help

  #103 opened a year ago by doi-vid
  1

• Updates for Midnight-IDT/V2 primer schemes

  #58 opened 2 years ago by llk578496
  3

• Problems process pipeline:runArtic

  #98 opened a year ago by Bioloko
  10

• MacOS M1 chip, sed making tmp file with wrong permissions and failure to export issue

  #100 opened a year ago by rebeelouise
  5

• errors from downloading epi2me wf

  #99 opened a year ago by devfidz
  1

• Regarding filtering of Low Frequency and Subclonal Mutations

  #68 opened 2 years ago by Rohit-Satyam
  4

• Consensus sequences are not produced even after good coverage

  #97 opened a year ago by Rohit-Satyam
  5

• Primer dropout with a suspected XBB.1.1 sequence

  #93 opened a year ago by iahdb
  5

• Unable to pull from repository

  #94 opened a year ago by llk578496
  2

• Option to output failed vcf

  #92 opened a year ago by ammaraziz
  1

• test

  #91 opened a year ago by mattdmem
  1

• Why I am getting a Command Trace Error

  #87 opened a year ago by navyn007
  4

• Midnight-ONT/V3 bed file

  #59 opened a year ago by wwlsung
  1

• ERROR ~ Error executing process > 'pipeline:report (1)'

  #88 opened a year ago by Habibk91
  2

• [enhancement]: wf-artic for other viruses - skip nextclade and pangolin

  #77 opened a year ago by sarahryter
  3

• Why I am getting a Command Trace Error

  #86 opened a year ago by navyn007
  1

• Inconsistent results

  #85 opened a year ago by phongphak
  2

• Question: Custom scheme Midnight-IDT/V2

  #81 opened a year ago by fwa93
  2

• Artic V5.3.2 primer scheme

  #80 opened a year ago by VLeducq
  5

• Are homoplasmic site masked when running wf-artic

  #63 opened a year ago by Rohit-Satyam
  2

• pipeline:runArtic (1)'

  #84 opened a year ago by Habibk91
  2

• [Bug]: Error executing process > 'pipeline:report (1)' when using sample_sheet

  #83 opened a year ago by davidbante
  3

• [enhancement:] wf-artic pipeline filters too many reads

  #65 opened a year ago by Rohit-Satyam
  1

• [Bug]: sed: couldn't open temporary file ./sed3unqLx: Permission denied

  #70 opened a year ago by corneliusroemer
  2

• [Bug]: publish output process refactoring recommended

  #74 opened a year ago by phyden
  1

• [Bug]: WARNING due to undefined param.threads

  #82 opened a year ago by ammaraziz
  1

• [Bug]: Error executing process > 'pipeline:report (1)'

  #79 opened a year ago by myorick
  1

• [Bug]: Problem with a custom scheme

  #78 opened 2 years ago by michallaz
  1

• [Bug]: epi2me-labs/wf-artic v0.3.22 EPI2ME Labs V4.1.2 workflow primer scheme selection

  #76 opened 2 years ago by PWSmit
  4

• [Bug]: wf-artic v0.3.21 on epi2melabs v4.0.0 looks for primer scheme in directory that doesn't exist

  #73 opened 2 years ago by kneubehl
  15

• [Bug]: Has medaka models updated to support v14 chemistry

  #75 opened 2 years ago by llk578496
  3

• [Bug]: FASTCAT command not found

  #66 opened 2 years ago by NHPttt
  1

• [Bug]: Process 'pipeline:pangolin' terminated

  #64 opened 2 years ago by leoncaly
  4

• [Bug]: Error `Trace file already exists` when rerunning command after failure

  #71 opened 2 years ago by corneliusroemer
  2

• [Bug]: Telemetry process takes much time

  #60 opened 2 years ago by mnemosymenicolas
  4

• [Bug]: not really a bug... a question

  #67 opened 2 years ago by arielamadio
  0

• Insights required in pipeline arguments and a feature request

  #62 opened 2 years ago by Rohit-Satyam
  5

• [Bug]: Error executing process > 'handleSingleFile

  #61 opened 2 years ago by Rohit-Satyam
  8