taxprofiler/taxpasta

Issues

• [BUG] MetaPhlAn 4 output with duplicate clade tax id is not supported

  #140 opened a year ago by MajoroMask
  16

• Should we support the OPAL format as output?

  #113 opened a year ago by Midnighter
  10

• [Feature] Add support for Sourmash

  #114 opened a year ago by Midnighter
  5

• [Feature] Allow to set threshold for compositionality check of Bracken results

  #73 opened 5 months ago by alexhbnr
  13

• [Feature] Adding metabarcoding/amplicon support

  #148 opened 6 months ago by paulzierep
  1

• [BUG] Metaphlan4 run error in Microba datasets

  #143 opened 7 months ago by minhtrung1997
  8

• Error with Biom format output from kraken2 report

  #144 opened 7 months ago by UmaJan
  4

• [Feature] add an option to let taxpasta report relative abundance as fractions instead of only counts

  #142 opened 10 months ago by Midnighter
  1

• [Feature] Changing/adding taxonomies on standardized profile tables

  #145 opened 7 months ago by Swindle98
  1

• [BUG] tax entries with `no rank` failed `--add-lineage`, `--add-id-lineage` or `--add-rank-lineage`

  #141 opened 10 months ago by MajoroMask
  2

• [BUG] (I think): "Unrecognized file type extension '.biom'"

  #138 opened 10 months ago by emilyvansyoc
  10

• [BUG] Adding taxon names to the output fails

  #137 opened a year ago by SannaAb
  6

• Allow ignoring profile errors when merging

  #135 opened a year ago by Midnighter
  0

• Add taxonomy to BIOM format

  #59 opened a year ago by Midnighter
  1

• [Feature] Add a taxonomy table to the BIOM output

  #133 opened a year ago by Midnighter
  0

• [Feature] Reverse the order of the current lineages

  #131 opened a year ago by Midnighter
  0

• [Feature] Add `--add-rank-lineage` to `taxpasta merge` and `taxpasta standardise`

  #126 opened a year ago by MajoroMask
  2

• [Feature] Add support for kmcp profiler

  #129 opened a year ago by sofstam
  0

• Issue regarding Taxpasta application in the kaiju classification tables.[BUG]

  #83 opened 2 years ago by LilyAnderssonLee
  6

• [Refactor] Provide an internal error hierarchy to simplify exception handling

  #127 opened a year ago by Midnighter
  0

• [BUG] Problem with kraken-type reports (from KrakenUniq)

  #123 opened a year ago by jfy133
  2

• [BUG] CRITICAL error when parsing MetaPhlAn4's output

  #111 opened a year ago by apcamargo
  2

• [Feature] Add support for ganon 'tre' report

  #108 opened a year ago by jfy133
  0

• [BUG] Certain parser problems are only warnings

  #100 opened a year ago by Midnighter
  0

• Avoid type coercion for domain models

  #102 opened a year ago by Midnighter
  0

• [BUG] Improve docs on tutorial data & warning against cross-profile merging

  #98 opened 2 years ago by jfy133
  0

• Duplicate taxIDs in mOTUs

  #46 opened 2 years ago by sofstam
  0

• Document that setting the output format overrules any given file extension

  #93 opened 2 years ago by Midnighter
  0

• Document a curl command to download sample files in the readme

  #92 opened 2 years ago by Midnighter
  0

• [BUG] Getting started tutorial is too complex

  #94 opened 2 years ago by jfy133
  0

• [BUG] taxpasta deletes nodes/names.dmp from --taxonomy dir

  #87 opened 2 years ago by kdm9
  5

• Add repostatus.org badge

  #90 opened 2 years ago by Midnighter
  0

• [BUG] Some internal links on readthedeocs broken

  #88 opened 2 years ago by jfy133
  0

• [Feature] Reorder columns after merging when options "--add-name/rank/lineage" and wide format are selected

  #81 opened 2 years ago by alexhbnr
  0

• Metaphlan3 output contains reads classified as taxid '-1' [BUG]

  #82 opened 2 years ago by prototaxites
  2

• [BUG] Bracken compositionality tolerance is too strict

  #75 opened 2 years ago by Midnighter
  0

• Document extras in installation docs

  #69 opened 2 years ago by Midnighter
  0

• [BUG] inconsistency formatting behaviour between standardise and merge

  #72 opened 2 years ago by jfy133
  4

• Add the Zenodo webhook and badge

  #68 opened 2 years ago by Midnighter
  1

• Auto-generate help output for command quick reference

  #47 opened 2 years ago by Midnighter
  0

• Kaiju documentation specifies incorrect input source

  #54 opened 2 years ago by jfy133
  0

• Variability in KrakenUniq output causes bugs

  #57 opened 2 years ago by jfy133
  0

• Make taxonomy identifiers integer always

  #38 opened 2 years ago by Midnighter
  1

• Rename MALT to MEGAN6

  #45 opened 2 years ago by jfy133
  1

• Add parquet as output table option

  #37 opened 2 years ago by Midnighter
  0

• Add Python 3.11 to the test matrix

  #39 opened 2 years ago by Midnighter
  0

• Expose the diamond profiler

  #36 opened 2 years ago by Midnighter
  0

• Support tool: KrakenUniq

  #18 opened 2 years ago by jfy133
  0

• Add support for kaiju-mergeOutputs

  #24 opened 2 years ago by jfy133
  0

• Add tests

  #22 opened 2 years ago by maxibor
  2