beiko-lab/arete

Issues

• Add UpSet plot script

  #200 opened 4 months ago by rbeiko
  0

• Add feature dispersion script

  #201 opened 4 months ago by rbeiko
  0

• Create new entries for the pipeline

  #143 opened a year ago by jvfe
  3

• Add outgroup genome parameter to the pipeline

  #57 opened a year ago by jvfe
  0

• Restore subsampled genomes after pan-genome inference

  #77 opened 2 years ago by rbeiko
  0

• Add BAKTA annotation results to rSPR output

  #168 opened a year ago by jvfe
  0

• Pipeline crashes when PopPUNK identifies only one lineage

  #113 opened a year ago by rbeiko
  0

• Change default resource requirements and add different resource profiles

  #150 opened a year ago by jvfe
  0

• Adjust phylogenomics output

  #146 opened a year ago by rbeiko
  0

• Allow the user to choose which columns get added to the feature profile

  #140 opened a year ago by jvfe
  0

• Change add_column/filter_matches processes to run with collected output

  #138 opened a year ago by jvfe
  0

• Add a sample ID check in samplesheet check

  #129 opened a year ago by jvfe
  0

• Let the user choose which tools to run in the annotation subworkflow

  #133 opened a year ago by jvfe
  0

• Automate phylogenomic analysis from Ppangolin output

  #126 opened a year ago by rbeiko
  1

• Add PhiSpy to annotation report and profile

  #123 opened a year ago by jvfe
  0

• Generalize how the mobsuite contig IDs are parsed by create_report.py

  #121 opened a year ago by jvfe
  0

• Replace VIBRANT with another prophage-prediction tool

  #115 opened a year ago by jvfe
  0

• VFDB short ID regex fails when more than three groups get captured

  #119 opened a year ago by jvfe
  0

• Chunked fasttree overwriting files when filename has '.'

  #117 opened a year ago by jvfe
  0

• Add module to create presence / absence pattern of features across genomes

  #110 opened a year ago by jvfe
  0

• Add cross-referencing/useful IDs for other DIAMOND dbs

  #108 opened a year ago by jvfe
  0

• Update RGI

  #109 opened a year ago by jvfe
  0

• Add ppanggolin as an alternative to Panaroo

  #106 opened 2 years ago by jvfe
  0

• Add other VFDB IDs in the annotation report

  #104 opened 2 years ago by jvfe
  0

• Create samplesheet for panaroo input

  #102 opened 2 years ago by jvfe
  0

• Create TSV report for annotation results

  #95 opened 2 years ago by jvfe
  0

• Header lines repeated in IntegronFinder output

  #99 opened 2 years ago by jvfe
  0

• Run RGI on Bakta's output

  #96 opened 2 years ago by jvfe
  0

• Add actual filtering to filter_alignment.py

  #92 opened 2 years ago by jvfe
  0

• Automate PopPunk genome scan

  #78 opened 2 years ago by rbeiko
  1

• Add module for heatmap of core/accessory thresholds and number of genomes

  #81 opened 2 years ago by jvfe
  0

• Create table with concatenated results from annotation

  #85 opened 2 years ago by jvfe
  1

• Error on missing samples

  #87 opened 2 years ago by fmaguire
  0

• Suggest using a different -entry if samplesheet fits that entry

  #88 opened 2 years ago by jvfe
  0

• Convert panaroo output to graphviz dot format

  #84 opened 2 years ago by jvfe
  0

• Use subsampled genomes only in the phylogenomics subworkflow

  #79 opened 2 years ago by jvfe
  0

• Make --poppunk_db flag optional in assembly/assembly_qc entries

  #80 opened 2 years ago by jvfe
  0

• CheckM execution failing on assemblyqc subworkflow

  #75 opened 2 years ago by jvfe
  0

• Add option to subsample similar genomes

  #60 opened 2 years ago by jvfe
  0

• Add Integron Finder

  #70 opened 2 years ago by jvfe
  0

• Add singularity to CI checks

  #72 opened 2 years ago by jvfe
  0

• VIBRANT DB download fails because of command line dependencies

  #68 opened 2 years ago by jvfe
  1

• Don't create figures when running VIBRANT

  #66 opened 2 years ago by jvfe
  0

• Add module for phage identification

  #59 opened 2 years ago by jvfe
  0

• Add genomic island detection to the workflow

  #64 opened 2 years ago by jvfe
  0

• Add alignment step against ICEberg2 db

  #58 opened 2 years ago by jvfe
  0

• Update Bakta module and add Bakta db download

  #53 opened 2 years ago by jvfe
  0

• Change panaroo default to be -a pan

  #46 opened 2 years ago by jvfe
  1

• Concatenate DIAMOND's results by DB

  #43 opened 2 years ago by jvfe
  0

• Add --light option to the workflow

  #42 opened 2 years ago by jvfe
  0