nf-core/bactmap

Issues

• pipeline fails when parameter trim = false

  #55 opened 2 years ago by craigwindell
  2

• calculation of snps to exclude LowQual positions

  #60 opened 2 years ago by jennahamlin
  0

• Cannot get property 'args' on null object error

  #53 opened 2 years ago by creamerk
  2

• Memory error

  #49 opened 2 years ago by MostafaYA
  8

• Modules required for DSL 2 implementation of pipeline

  #6 opened 3 years ago by antunderwood
  0

• Add documentation

  #28 opened 3 years ago by antunderwood
  0

• Add pseudogenome count check before running gubbins

  #22 opened 3 years ago by antunderwood
  0

• Option to downsample before fastp

  #44 opened 3 years ago by antunderwood
  0

• option to keep the trimmed reads

  #43 opened 3 years ago by antunderwood
  0

• download reads from the SRA/ENA

  #42 opened 3 years ago by antunderwood
  0

• raxml-ng DSL2 module

  #15 opened 3 years ago by antunderwood
  0

• Incorporate nf-core modules into bactmap

  #26 opened 3 years ago by antunderwood
  0

• iqtree DSL2 module

  #14 opened 3 years ago by antunderwood
  0

• mash sketch DSL2 module

  #7 opened 3 years ago by antunderwood
  0

• seqtk sample DLS2 module

  #8 opened 3 years ago by antunderwood
  1

• fasttree DSL2 module

  #13 opened 3 years ago by antunderwood
  0

• snp-sites DSL2 module

  #11 opened 3 years ago by antunderwood
  0

• rapidnj DSL2 module

  #12 opened 3 years ago by antunderwood
  0

• rasusa DSL2 module

  #17 opened 3 years ago by thanhleviet
  1

• Test singularity

  #21 opened 3 years ago by antunderwood
  0

• Test docker

  #20 opened 3 years ago by antunderwood
  0

• bcftools call DSL2 module

  #9 opened 3 years ago by antunderwood
  0

• gubbins DSL2 module

  #10 opened 3 years ago by antunderwood
  0

• BACTMAP: Convert all param docs to JSON schema

  #5 opened 3 years ago by apeltzer
  0

• Missing TEMPLATE branch

  #3 opened 5 years ago by maxulysse
  0