nf-core/funcscan

Issues

• funcscan -profile test failed

  #414 opened 2 months ago by asogg
  2

• Optimize antismash usage docs

  #313 opened 2 months ago by jasmezz
  1

• comBGC column BGC_length inaccurate

  #399 opened 4 months ago by martinklapper
  3

• Add missing essential parameters for antismash

  #356 opened 4 months ago by Darcy220606
  4

• improving tool documentation & adding tests

  #383 opened 5 months ago by ewissel
  1

• Benchmarking tests showing resource values are suboptimal

  #292 opened a year ago by jfy133
  0

• Apply nf-test on funcscan

  #280 opened 4 months ago by louperelo
  1

• nf-test wishlist

  #398 opened 4 months ago by jasmezz
  0

• A special samplesheet can delete all my sequences

  #395 opened 4 months ago by Microbion
  3

• Antismash parameter bug

  #390 opened 4 months ago by ewissel
  1

• Missing icons for BGC sections in nextflow schema/parameter docs

  #380 opened 4 months ago by jfy133
  0

• Consider allowing annotation to run even if downstream screening not run

  #392 opened 4 months ago by jfy133
  0

• Workflow diagram is broken in `dev`

  #364 opened 4 months ago by jfy133
  1

• Missing Annotation files

  #389 opened 4 months ago by xeniaroda29
  2

• GUNZIP module is confused by repeated patterns in sample name and fasta path.

  #367 opened 5 months ago by m3hdad
  2

• Missing abricate database download instructions in usage

  #379 opened 5 months ago by jfy133
  0

• The spliting of contigs into _long and _short should only be performed when needed, or at least it should be skippable

  #378 opened 5 months ago by amizeranschi
  1

• Update AMPcombi to version 0.2.1

  #336 opened 5 months ago by Darcy220606
  1

• Mention AMPcombi and DRAMP database in usage.md

  #354 opened 5 months ago by jasmezz
  2

• A uniform input for all tools in each screening workflow

  #385 opened 5 months ago by m3hdad
  2

• In some cases RGI will not produce all files expected for mving for publishing

  #376 opened 6 months ago by jfy133
  5

• AMPLIFY_PREDICT exits with a ValueError while checking input

  #373 opened 6 months ago by m3hdad
  1

• deeparg 1.0.4 required to correctly fetch DBs

  #370 opened 6 months ago by m3hdad
  1

• Amrfinderplus_update not working in test run

  #328 opened 6 months ago by pdy1084
  4

• Remove warning about broken DeepBGC database links from docs

  #355 opened 6 months ago by jasmezz
  1

• Fix BAKTA publish dir

  #357 opened 6 months ago by Darcy220606
  1

• Split input assemblies into BGC vs ARG/AMP compatible length types

  #360 opened 6 months ago by jfy133
  1

• Reorder/rename hamronization summary columns

  #333 opened 7 months ago by Darcy220606
  0

• Include Contig taxonomic classification before going into the summary modules

  #318 opened 7 months ago by Darcy220606
  1

• URGENT: pin nf-validation version

  #342 opened 7 months ago by nvnieuwk
  2

• Adapt deepBGC to use GPUs

  #326 opened a year ago by Darcy220606
  4

• Update hAMRonization to v1.1.4

  #321 opened 8 months ago by louperelo
  1

• Upgrade `antiSMASH` from v6.1.1 to v7.0

  #282 opened 8 months ago by Darcy220606
  2

• Add BAKTA results to MultiQC

  #339 opened 9 months ago by jfy133
  0

• Add ability to unzip a archived version of the deepARG database as input

  #319 opened 9 months ago by jfy133
  2

• Update Bakta to 1.9.2

  #325 opened 9 months ago by jasmezz
  2

• Drop trailing `.0` of workflow metromap

  #287 opened 9 months ago by jfy133
  1

• DEEPARG container not compatible with new nf-core template container options (2.12)

  #337 opened 9 months ago by jfy133
  1

• Add module: resfinder

  #330 opened 10 months ago by jasmezz
  0

• Add pharokka to nf-core/funcscan

  #329 opened a year ago by CarsonJM
  0

• Add parameter after annotation for aa length

  #312 opened a year ago by Darcy220606
  0

• Check DRAMP db download folder

  #271 opened a year ago by louperelo
  1

• Update Bakta to v.1.8.1

  #293 opened a year ago by Darcy220606
  1

• change PROKKA default to retain original contig names

  #305 opened a year ago by Darcy220606
  0

• Remove unnecessary figures

  #315 opened a year ago by jasmezz
  1

• Error with uncompressed FASTA files

  #309 opened a year ago by tavareshugo
  2

• Pigz error with pyrodigal

  #291 opened a year ago by jasmezz
  7

• Add dynamic citations of pipeline run tools in MultiQC report

  #284 opened a year ago by jfy133
  1

• Consider adding annotation tools to MultiQC report

  #277 opened a year ago by jfy133
  0

• Incorrect docker container uris

  #281 opened a year ago by sunitj
  6