fmalmeida/bacannot

Issues

• Update integron finder tool version

  #120 opened 9 months ago by fmalmeida
  1

• Include Phylogeny?

  #124 opened 4 months ago by fmalmeida
  1

• Add pgpg_finder

  #123 opened 5 months ago by fmalmeida
  0

• Add Bactabolize tool

  #122 opened 6 months ago by fmalmeida
  0

• add tool: pharokka

  #57 opened 2 years ago by fmalmeida
  0

• MLST step failed

  #92 opened 8 months ago by Moana63
  8

• generate a new (updated) pre-built pipeline database

  #97 opened 8 months ago by fmalmeida
  2

• emote origin did not advertise Ref for branch refs/heads/116-integron_finder_2gff-terminated-with-an-error

  #118 opened 9 months ago by JavariaAshraf
  20

• BACANNOT:INTEGRON_FINDER_2GFF (vibrio9)` terminated with an error exit status (255)

  #116 opened 9 months ago by JavariaAshraf
  10

• Update Zenodo Project distributed with Paper

  #114 opened a year ago by fmalmeida
  0

• Error on SUMMARY step when missing annotation/id.txt key

  #111 opened a year ago by mladen5000
  7

• Wrap-up `dev` and release v3.3

  #88 opened a year ago by fmalmeida
  12

• Duplicate reads to Unique read names...

  #107 opened a year ago by Michaelijesse
  4

• Update pipeline docker images from docker tags to docker shasum

  #100 opened a year ago by fmalmeida
  1

• Include ICEs and prophage annotation in json summary

  #98 opened a year ago by fmalmeida
  2

• PacBio Genome Assembly - Low - Compared to its Reference

  #105 opened a year ago by Michaelijesse
  0

• Feature request: Add reads de-duplication step before assembly

  #104 opened a year ago by Michaelijesse
  8

• Summary

  #102 opened a year ago by CarmenMartinezSeijas
  5

• Include known issue form #96 in the Readme

  #99 opened a year ago by fmalmeida
  0

• Error Summary

  #96 opened a year ago by josefdiaz
  12

• Tools to use own docker image

  #69 opened a year ago by fmalmeida
  3

• Add dbscan-swa tool

  #95 opened a year ago by fmalmeida
  0

• Prokka module can get after modules stuck if the header file longer than 20 and not separated by tab or space

  #85 opened 2 years ago by minhtrung1997
  7

• add tool: MOB-suite

  #81 opened 2 years ago by fmalmeida
  2

• add tool: integron finder 2.0

  #50 opened 2 years ago by fmalmeida
  7

• AMR Finder get error

  #86 opened 2 years ago by minhtrung1997
  6

• Resource error (139,140,...) when run on slurm HPC

  #79 opened 2 years ago by minhtrung1997
  3

• TypeError raised by falmedia.py

  #84 opened 2 years ago by wonitawowowo
  4

• Provide databases as a .tar.gz

  #80 opened 2 years ago by fmalmeida
  2

• Issue in KOFam database download

  #78 opened 2 years ago by minhtrung1997
  13

• enhance circos plot

  #77 opened 2 years ago by fmalmeida
  0

• Custom database report file bugs

  #68 opened 2 years ago by lam-c
  13

• module for generating circos plot for contigs

  #70 opened 2 years ago by fmalmeida
  9

• Upgrade Bakta to 1.5.1+

  #75 opened 2 years ago by sunitj
  4

• Use ICEO for ICE prediction?

  #73 opened 2 years ago by fmalmeida
  0

• Issue with Antismash

  #71 opened 2 years ago by fetyj
  10

• Report failed

  #66 opened 2 years ago by fetyj
  2

• Use of named outputs in processes

  #39 opened 2 years ago by abhi18av
  10

• problem with ResFinder annotation "merge"

  #64 opened 2 years ago by fmalmeida
  0

• ISLANDPATH failed when there is no CDS in Bakta annotated gbk file

  #62 opened 2 years ago by rujinlong
  5

• workflow unsuccessful

  #54 opened 2 years ago by fetyj
  19

• Database downloading

  #52 opened 2 years ago by fetyj
  9

• re-think modules organization and structure

  #36 opened 3 years ago by fmalmeida
  15

• add tool: f5c (methylation)

  #47 opened 3 years ago by fmalmeida
  0

• provide a small dataset for quick code tests

  #46 opened 3 years ago by fmalmeida
  9

• Change case of modules/workflows to distinguish them from parameters

  #38 opened 3 years ago by abhi18av
  13

• Split the configuration into multiple profiles with a dedicated folder

  #37 opened 3 years ago by abhi18av
  3

• possibility to set a global resfinder species value for samples in YAML

  #33 opened 3 years ago by fmalmeida
  2

• also accept samplesheet in CSV/TSV

  #41 opened 3 years ago by fmalmeida
  0

• diminish pipeline complexity: pass sample always with YAML

  #35 opened 3 years ago by fmalmeida
  6