BCCDC-PHL/ncov2019-artic-nf

Issues

• Pipeline fails on empty fastq input

  #55 opened a year ago by dfornika
  1

• Add support for SampleSheet input

  #53 opened a year ago by dfornika
  1

• Make sure all processes use DSL2-compatible syntax

  #52 opened 2 years ago by dfornika
  0

• Viral contig name is hard-coded in `callConsensusFreebayes` process

  #50 opened 2 years ago by dfornika
  0

• Downsampling script may fail with `IndexError`

  #48 opened 2 years ago by dfornika
  1

• UTR trimming sites are hard-coded

  #49 opened 2 years ago by dfornika
  0

• Process `downsampleBamToFastq` may fail when `/tmp` filesystem is full

  #46 opened 3 years ago by dfornika
  0

• No consensus file created when all reads removed before alignment

  #44 opened 4 years ago by dfornika
  0

• Add testing pipeline to run on commits to master

  #42 opened 4 years ago by dfornika
  0

• fastq files not found

  #35 opened 4 years ago by dfornika
  2

• Get CI testing working

  #40 opened 4 years ago by dfornika
  0

• Use consistent extension for both consensus fasta files

  #36 opened 4 years ago by dfornika
  0

• Rename outputs downstream of consensus generation

  #37 opened 4 years ago by dfornika
  0

• Remove unnecessary configs

  #38 opened 4 years ago by dfornika
  0

• Add freebayes variant calling

  #32 opened 4 years ago by dfornika
  0

• Incorporate GFF file

  #31 opened 4 years ago by dfornika
  1

• Normalise or downsample high-coverage samples

  #29 opened 4 years ago by dfornika
  3

• Evaluate changes from upstream repos for inclusion here

  #1 opened 4 years ago by dfornika
  4

• filter_non_human_reads.py: ZeroDivisionError

  #26 opened 4 years ago by dfornika
  0

• Routinely align consensus against MN908947.3 reference

  #2 opened 4 years ago by dfornika
  1

• Update to ivar-1.3 with fix for primer trimming

  #6 opened 4 years ago by dfornika
  0

• Add host sequence removal (dehosting) step

  #7 opened 4 years ago by dfornika
  0

• Filter residual adapters

  #17 opened 4 years ago by dfornika
  0

• Remove CLIMB-specific steps

  #18 opened 4 years ago by dfornika
  0

• Increase minimum length of reads to keep after primer trimming

  #19 opened 4 years ago by dfornika
  0

• Routinely index .bam files as they are generated

  #22 opened 4 years ago by dfornika
  0

• Replace 'qc_pass_climb_upload' output directory with 'nml_upload' directory

  #24 opened 4 years ago by dfornika
  0

• Run tests on PRs against 'development' branch

  #20 opened 4 years ago by dfornika
  1