BCCDC-PHL/FluViewer

Issues

• When segment is not within range, log the segment length along with the expected range

  #46 opened 4 months ago by dfornika
  0

• Analysis crashes during `blast_contigs` stage if 0 contigs are found for a segment

  #41 opened 4 months ago by dfornika
  0

• Keep "analysis stage indexes" consistent whether or not depth normalization is skipped

  #43 opened 4 months ago by dfornika
  0

• Make bbnorm-based normalization optional

  #24 opened 5 months ago by dfornika
  1

• Incompatibility between `spades=3.15.*` and `setuptools=70.*`

  #37 opened 5 months ago by dfornika
  1

• Update provided environment.yaml file to produce a self-contained and complete FluViewer conda env

  #35 opened 5 months ago by dfornika
  0

• Support analysis of Influenza B sequence data

  #23 opened 5 months ago by dfornika
  4

• Add support for long (nanopore) read input

  #34 opened 5 months ago by dfornika
  0

• Analysis fails when attempting to create a scaffolding plot for a segment for which there is no data.

  #32 opened 5 months ago by dfornika
  0

• Allow user to force writing outputs into existing output directory

  #29 opened 5 months ago by jpalmer37
  2

• Add CLI option to easily obtain fluviewer version

  #28 opened 5 months ago by jpalmer37
  0

• Analysis fails when blast database files do not already exist

  #25 opened 5 months ago by dfornika
  0

• Create plots to illustrate scaffolding process

  #21 opened 5 months ago by dfornika
  0

• Expand/improve documentation

  #20 opened 5 months ago by dfornika
  0

• Generate documentation

  #16 opened 5 months ago by dfornika
  0

• Re-organize outputs by 'analysis stage'

  #14 opened 5 months ago by dfornika
  0

• Add CI testing workflow(s)

  #13 opened 6 months ago by dfornika
  0

• Use argparse for command-line argument parsing

  #10 opened 6 months ago by dfornika
  0

• Improve logging

  #11 opened 6 months ago by dfornika
  0

• Simplify `environment.yml` file

  #8 opened 6 months ago by dfornika
  0

• Pull in latest FluViewer Release(s)

  #5 opened a year ago by dfornika
  0

• Coverage drop-outs leading to samples not being compete enough for tree

  #3 opened a year ago by JamesZlosnik
  0

• Make pip-installable

  #1 opened a year ago by dfornika
  0