iqbal-lab-org/viridian

Issues

• Documentation question

  #114 opened 2 months ago by iqbal-lab
  2

• Automatic amplicon scheme selection always fails when only one scheme is available

  #111 opened 7 months ago by bede
  1

• --ena_run causes crash unless --tech also used

  #108 opened 8 months ago by martinghunt
  0

• Example of sample placed wholly differently by Viridian in SA

  #63 opened 9 months ago by iqbal-lab
  2

• Rename repository to "viridian"

  #106 opened 2 years ago by martinghunt
  0

• Scheme detection fails depending on read order

  #90 opened 2 years ago by bede
  9

• More informative error messages for assembly failures

  #103 opened 2 years ago by bede
  0

• Handling adapter sequences

  #101 opened 2 years ago by martinghunt
  9

• Singularity build failing

  #95 opened 2 years ago by martinghunt
  4

• Deciding when to exclude primers

  #99 opened 2 years ago by martinghunt
  15

• Primers contributing to Clean.Tot.cons

  #100 opened 2 years ago by martinghunt
  7

• Consistent use of primers throughout pipeline

  #102 opened 2 years ago by martinghunt
  6

• If users want to force scheme, let them

  #87 opened 2 years ago by iqbal-lab
  5

• Version string in refactor_2022

  #97 opened 2 years ago by jeff-k
  0

• Cuckoo mode as a command-line option

  #82 opened 2 years ago by iqbal-lab
  14

• Update JSON with summary block/new info while preserving tags used by GPAS

  #94 opened 2 years ago by iqbal-lab
  2

• JSON log - multiple small things

  #83 opened 2 years ago by iqbal-lab
  0

• Format changes/cleanup of the TSV file

  #92 opened 2 years ago by iqbal-lab
  14

• Immediate issues to be combined into new tag for testing

  #79 opened 2 years ago by iqbal-lab
  4

• Consensus filename should match the README and 0.3.7

  #86 opened 2 years ago by iqbal-lab
  3

• keep-bam option should make a coord sorted indexed bam not name-sorted

  #84 opened 2 years ago by iqbal-lab
  0

• VCF mods

  #93 opened 2 years ago by iqbal-lab
  0

• Homopolymer filter for nanopore data

  #80 opened 2 years ago by iqbal-lab
  1

• Compare two primer/amplicon filter options

  #81 opened 2 years ago by iqbal-lab
  9

• Output of tsv as commandline option

  #89 opened 2 years ago by iqbal-lab
  1

• errors in installation.

  #91 opened 2 years ago by hafizmtalha
  1

• Enumerate what is happening in the extra indel errors in validation set

  #88 opened 2 years ago by iqbal-lab
  0

• Delete temp files by default

  #85 opened 2 years ago by iqbal-lab
  0

• Suitability of 'Sydney' scheme for autodetection

  #77 opened 2 years ago by bede
  3

• Cope gracefully if passed empty fastq

  #78 opened 2 years ago by iqbal-lab
  0

• Site to check in 0.9 SA viridian/G trees - N63

  #54 opened 2 years ago by iqbal-lab
  1

• Site to check in 0.9 SA viridian/G trees - N203

  #55 opened 2 years ago by iqbal-lab
  1

• Site to check in 0.9 SA viridian/G trees - N204

  #56 opened 2 years ago by iqbal-lab
  1

• Site to check in 0.9 SA viridian/G trees - N215

  #57 opened 2 years ago by iqbal-lab
  1

• Site to check in 0.9 SA viridian/G trees - N235 in B.1.1.7

  #58 opened 2 years ago by iqbal-lab
  1

• Site to check in 0.9 SA viridian/G trees - N377

  #59 opened 2 years ago by iqbal-lab
  1

• Site to check in 0.9 SA viridian/G trees - N413

  #60 opened 2 years ago by iqbal-lab
  1

• Site to check in 0.9 SA viridian/G trees - something weird in C.1.2 at E21

  #61 opened 2 years ago by iqbal-lab
  1

• What is happening in SRR17712969 at M3

  #62 opened 2 years ago by iqbal-lab
  1

• SRR16298636 looks odd at M20

  #64 opened 2 years ago by iqbal-lab
  1

• M82 is a mess for everyone

  #65 opened 2 years ago by iqbal-lab
  1

• Anomalies at M155

  #66 opened 2 years ago by iqbal-lab
  1

• Not quite perfectly clean at nt210

  #67 opened 2 years ago by iqbal-lab
  1

• Good example at nt241

  #68 opened 2 years ago by iqbal-lab
  2

• Spike 215 looking odd in both illumina and nanopore

  #69 opened 2 years ago by iqbal-lab
  1

• Worse/noiser performance with nanopore at Orf7a:82

  #70 opened 2 years ago by iqbal-lab
  1

• Coordinate 22227 worth evaluating carefully

  #71 opened 2 years ago by iqbal-lab
  1

• Ampliseq digests primers

  #74 opened 2 years ago by iqbal-lab
  0

• Known issues with ARTIC3 in vocs

  #73 opened 2 years ago by iqbal-lab
  0

• Site to check in 0.9 SA viridian/G trees - N13

  #53 opened 3 years ago by iqbal-lab
  0