cfe-lab/MiCall

Issues

• Simplify comparison of project definitions

  #1158 opened a month ago by donkirkby
  0

• Reimplement the stitcher

  #1030 opened 8 months ago by Donaim
  6

• Ensure that collated subdirectories are archived deterministically

  #1150 opened 2 months ago by Donaim
  2

• Fix retry logic in `qai_upload.py`

  #1140 opened 3 months ago by Donaim
  1

• Pin GitHub Actions to digests

  #1135 opened 4 months ago by jhrozek
  0

• Evidence for joins in contigs

  #764 opened 3 years ago by donkirkby
  0

• New MiSeq software

  #843 opened 2 years ago by donkirkby
  0

• Collate outputs in Kive

  #876 opened 2 years ago by donkirkby
  1

• Feature Proposal: a Merger Tool

  #1036 opened 9 months ago by Donaim
  1

• Sample sheet parser fails when enum contains an underscore

  #888 opened 2 years ago by CBeelen
  2

• Add HIV-AD project code

  #998 opened a year ago by donkirkby
  2

• Stop using deprecated Bio.Application

  #1107 opened 6 months ago by Donaim
  0

• Add documentation describing the new stitcher.

  #1089 opened 6 months ago by Donaim
  0

• Update to Python 3.11

  #981 opened a year ago by CBeelen
  0

• Aligning to defective start codon in `vpu`

  #1024 opened a year ago by Donaim
  0

• Write `conseq_ins_csv` to the output directory

  #1085 opened 7 months ago by Donaim
  0

• Refactor the visualizer to make it at least somewhat readable.

  #1086 opened 7 months ago by Donaim
  0

• Remove old stitching code.

  #1087 opened 7 months ago by Donaim
  0

• Multiple python interpreters in dev container cause issues

  #1033 opened a year ago by Donaim
  4

• Visualize stitched consensus

  #1016 opened 8 months ago by donkirkby
  2

• Download the new proviral_landscape.csv

  #984 opened a year ago by CBeelen
  0

• Large insertion / messy alignments in nef cause problems in conseq_stitched.csv

  #786 opened 8 months ago by CBeelen
  1

• Upload HIVSeqinR

  #844 opened 2 years ago by donkirkby
  1

• Update minimap2 to the newest version

  #840 opened 3 years ago by CBeelen
  1

• Update to drawsvg 2.x

  #938 opened a year ago by CBeelen
  0

• Pin merge-mates to a tag?

  #893 opened 2 years ago by CBeelen
  0

• Update HIVdb to 9.4

  #884 opened a year ago by donkirkby
  1

• Add capsid gene region for CAI drug class

  #972 opened a year ago by CBeelen
  0

• Insertion counts for small insertions that change the reading frame

  #836 opened 3 years ago by CBeelen
  0

• Add insertion sequence to nuc.csv and amino.csv

  #768 opened 3 years ago by CBeelen
  0

• Stitched conseq: Conflicts between regions

  #778 opened a year ago by CBeelen
  2

• Score alignments?

  #826 opened 3 years ago by CBeelen
  0

• Improve coordinate concordance

  #965 opened a year ago by CBeelen
  0

• Proviral upload into QAI fails

  #886 opened 2 years ago by CBeelen
  1

• Plotting contigs fails due to alignment ending with insertion

  #887 opened a year ago by CBeelen
  1

• Concordance plot is shifted

  #963 opened a year ago by donkirkby
  0

• Small alignment leads to error in consensus aligner

  #899 opened 2 years ago by CBeelen
  3

• Resistance run fails on Kive if the input files have already been purged

  #921 opened 2 years ago by CBeelen
  0

• Missing insertion counts in vpr behind the skip position

  #850 opened 2 years ago by CBeelen
  1

• Concordance measures for regions

  #821 opened 3 years ago by CBeelen
  1

• Add HIV references for Ghana strains

  #806 opened 3 years ago by donkirkby
  0

• HCV reference genome has different region coordinates from individual seed references

  #794 opened 3 years ago by CBeelen
  1

• KeyError in update_qai.py

  #792 opened 3 years ago by CBeelen
  6

• Resistance runs failing for Covid

  #793 opened 3 years ago by CBeelen
  1

• Project scoring does not have new project codes yet

  #790 opened 3 years ago by CBeelen
  0

• Outputs in the wrong order in Singularity file

  #788 opened 3 years ago by CBeelen
  0

• Problem with multiple project codes

  #789 opened 3 years ago by CBeelen
  0

• Add stitched consensus

  #745 opened 3 years ago by donkirkby
  1

• Failure plotting genome coverage

  #743 opened 3 years ago by donkirkby
  1

• Minimap2 hits overlap in genome diagram

  #738 opened 3 years ago by donkirkby
  0