Ecosyste.ms: Issues

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GitHub / taxprofiler/taxpasta issues and pull requests

#154 - [Question] Possible to ignore NaN error caused by blank taxonomy_lvl during taxpasta merge?

Issue - State: open - Opened by Nkirc 24 days ago - 2 comments
Labels: question

#153 - Fix metaphlan profiles with duplicate entries by aggregating them

Pull Request - State: open - Opened by Midnighter 3 months ago - 6 comments

#152 - Fix mistake in docs for KrakenUniq regarding which parameter to use

Pull Request - State: closed - Opened by jfy133 6 months ago - 2 comments

#151 - Fix style in accordance with ruff

Pull Request - State: closed - Opened by Midnighter 6 months ago

#150 - Upgrade from cookiecutter

Pull Request - State: closed - Opened by Midnighter 6 months ago - 1 comment

#149 - feat: change output of BIOM format

Pull Request - State: closed - Opened by Midnighter 8 months ago

#148 - [Feature] Adding metabarcoding/amplicon support

Issue - State: open - Opened by paulzierep 9 months ago - 1 comment
Labels: enhancement, help wanted

#147 - Warn compositionality

Pull Request - State: closed - Opened by Midnighter 10 months ago - 2 comments

#146 - docs: add FAQ section to the documentation

Pull Request - State: closed - Opened by Midnighter 10 months ago - 1 comment
Labels: documentation

#145 - [Feature] Changing/adding taxonomies on standardized profile tables

Issue - State: open - Opened by Swindle98 10 months ago - 1 comment
Labels: enhancement, need info

#144 - Error with Biom format output from kraken2 report

Issue - State: closed - Opened by UmaJan 12 months ago - 4 comments
Labels: question

#143 - [BUG] Metaphlan4 run error in Microba datasets

Issue - State: closed - Opened by minhtrung1997 about 1 year ago - 8 comments
Labels: bug

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

Issue - State: open - Opened by Midnighter about 1 year ago - 1 comment
Labels: enhancement

#140 - [BUG] MetaPhlAn 4 output with duplicate clade tax id is not supported

Issue - State: open - Opened by MajoroMask over 1 year ago - 18 comments
Labels: bug

#139 - fix: repair adding tax info to results

Pull Request - State: closed - Opened by Midnighter over 1 year ago - 2 comments

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

Issue - State: closed - Opened by emilyvansyoc over 1 year ago - 10 comments
Labels: bug

#137 - [BUG] Adding taxon names to the output fails

Issue - State: closed - Opened by SannaAb over 1 year ago - 6 comments
Labels: bug

#136 - Allow ignoring profile errors when merging, message on empty profile

Pull Request - State: closed - Opened by Midnighter over 1 year ago - 1 comment

#135 - Allow ignoring profile errors when merging

Issue - State: closed - Opened by Midnighter over 1 year ago
Labels: enhancement

#134 - Feat biom tax table

Pull Request - State: closed - Opened by Midnighter over 1 year ago - 1 comment

#133 - [Feature] Add a taxonomy table to the BIOM output

Issue - State: closed - Opened by Midnighter over 1 year ago
Labels: enhancement

#132 - Fix reverse lineage

Pull Request - State: closed - Opened by Midnighter over 1 year ago

#131 - [Feature] Reverse the order of the current lineages

Issue - State: closed - Opened by Midnighter over 1 year ago
Labels: enhancement

#130 - Feat: add rank lineage

Pull Request - State: closed - Opened by Midnighter over 1 year ago - 6 comments

#129 - [Feature] Add support for kmcp profiler

Issue - State: closed - Opened by sofstam over 1 year ago
Labels: enhancement

#128 - Start adding kmcp profiler

Pull Request - State: closed - Opened by sofstam over 1 year ago - 7 comments

#127 - [Refactor] Provide an internal error hierarchy to simplify exception handling

Issue - State: open - Opened by Midnighter over 1 year ago
Labels: enhancement

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

Issue - State: closed - Opened by MajoroMask over 1 year ago - 2 comments
Labels: enhancement

#125 - Add Joss citation badge

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 3 comments

#124 - fix: force parsing specific columns as float

Pull Request - State: closed - Opened by Midnighter over 1 year ago - 1 comment

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

Issue - State: closed - Opened by jfy133 over 1 year ago - 2 comments
Labels: bug

#122 - chore: add citation file

Pull Request - State: closed - Opened by Midnighter over 1 year ago - 3 comments

#121 - Address editor comments

Pull Request - State: closed - Opened by jfy133 over 1 year ago

#120 - Fix date format

Pull Request - State: closed - Opened by xuanxu over 1 year ago - 1 comment

#119 - Use no-test logo for website header

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#118 - Add figure

Pull Request - State: closed - Opened by Midnighter over 1 year ago

#117 - Improve logos

Pull Request - State: closed - Opened by Midnighter over 1 year ago

#116 - Add PyOpenSci badge

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#115 - Adds a range of images

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#114 - [Feature] Add support for Sourmash

Issue - State: open - Opened by Midnighter over 1 year ago - 5 comments
Labels: enhancement

#113 - Should we support the OPAL format as output?

Issue - State: open - Opened by Midnighter over 1 year ago - 10 comments
Labels: enhancement

#112 - Minor grammartical and phrasing fixes

Pull Request - State: closed - Opened by jfy133 over 1 year ago

#111 - [BUG] CRITICAL error when parsing MetaPhlAn4's output

Issue - State: closed - Opened by apcamargo over 1 year ago - 2 comments
Labels: bug

#110 - Moritz review

Pull Request - State: closed - Opened by Midnighter over 1 year ago - 2 comments

#109 - Add support for ganon

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 5 comments

#108 - [Feature] Add support for ganon 'tre' report

Issue - State: closed - Opened by jfy133 over 1 year ago
Labels: enhancement

#107 - Support Metaphlan4 format

Pull Request - State: closed - Opened by TheOafidian over 1 year ago - 5 comments

#106 - Comments and suggestiosn on whole manuscript

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#105 - Add first suggestions

Pull Request - State: closed - Opened by sofstam over 1 year ago

#104 - Paper: Changes/suggations on affiliations/acknowledgements/summary

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 1 comment

#103 - WIP: fix links by using relative ones to markdown files

Pull Request - State: closed - Opened by Midnighter over 1 year ago - 5 comments
Labels: bug, documentation

#102 - Avoid type coercion for domain models

Issue - State: open - Opened by Midnighter over 1 year ago
Labels: enhancement

#101 - feat: raise parser warning as exception

Pull Request - State: closed - Opened by Midnighter over 1 year ago - 2 comments

#100 - [BUG] Certain parser problems are only warnings

Issue - State: closed - Opened by Midnighter over 1 year ago
Labels: bug

#99 - Address #98.

Pull Request - State: closed - Opened by jfy133 almost 2 years ago - 2 comments

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

Issue - State: closed - Opened by jfy133 almost 2 years ago
Labels: bug

#97 - Add curl commands to quickly fetch example files

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 2 comments

#96 - docs: improve description of options behavior

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 1 comment

#95 - Split up getting started to simplified version and deep dive

Pull Request - State: closed - Opened by jfy133 almost 2 years ago - 1 comment

#94 - [BUG] Getting started tutorial is too complex

Issue - State: closed - Opened by jfy133 almost 2 years ago
Labels: bug

#93 - Document that setting the output format overrules any given file extension

Issue - State: closed - Opened by Midnighter almost 2 years ago
Labels: documentation

#92 - Document a curl command to download sample files in the readme

Issue - State: closed - Opened by Midnighter almost 2 years ago
Labels: documentation

#91 - Add repostatus.org badge

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 1 comment
Labels: documentation

#90 - Add repostatus.org badge

Issue - State: closed - Opened by Midnighter almost 2 years ago

#89 - Fix all links

Pull Request - State: closed - Opened by jfy133 almost 2 years ago - 1 comment
Labels: documentation

#88 - [BUG] Some internal links on readthedeocs broken

Issue - State: closed - Opened by jfy133 almost 2 years ago
Labels: bug

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

Issue - State: closed - Opened by kdm9 almost 2 years ago - 5 comments
Labels: bug

#86 - Insert taxonomic information in a more suitable column order

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 1 comment

#85 - Fix metaphlan tax ID being -1 and combine all unclassified counts

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 1 comment

#84 - refactor: generally allow 1% tolerance of compositionality

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 2 comments

#83 - Issue regarding Taxpasta application in the kaiju classification tables.[BUG]

Issue - State: closed - Opened by LilyAnderssonLee almost 2 years ago - 6 comments
Labels: bug

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

Issue - State: closed - Opened by prototaxites almost 2 years ago - 2 comments
Labels: bug

#80 - Render without rich

Pull Request - State: closed - Opened by Midnighter almost 2 years ago

#79 - Documentation: minor typo fixes and phrasing tweaks

Pull Request - State: closed - Opened by jfy133 almost 2 years ago - 2 comments

#78 - Note on terminology and background

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 1 comment

#77 - Post-tutorial cleanup

Pull Request - State: closed - Opened by Midnighter almost 2 years ago

#76 - fix: increase the tolerance when comparing floats

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 1 comment

#75 - [BUG] Bracken compositionality tolerance is too strict

Issue - State: closed - Opened by Midnighter almost 2 years ago
Labels: bug

#74 - fix: correctly set the version according to hatch-vcs

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 1 comment

#73 - [Feature] Allow to set threshold for compositionality check of Bracken results

Issue - State: closed - Opened by alexhbnr almost 2 years ago - 13 comments
Labels: enhancement

#72 - [BUG] inconsistency formatting behaviour between standardise and merge

Issue - State: open - Opened by jfy133 almost 2 years ago - 4 comments
Labels: bug

#71 - Delete tutorial.qmd

Pull Request - State: closed - Opened by jfy133 almost 2 years ago - 1 comment

#70 - Document optional dependencies

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 4 comments
Labels: documentation

#69 - Document extras in installation docs

Issue - State: closed - Opened by Midnighter almost 2 years ago
Labels: documentation

#68 - Add the Zenodo webhook and badge

Issue - State: closed - Opened by Midnighter almost 2 years ago - 1 comment

#67 - fix: provide files directly to `TaxDb`

Pull Request - State: closed - Opened by Midnighter almost 2 years ago

#66 - Add longer/detailed Tutorial

Pull Request - State: closed - Opened by jfy133 almost 2 years ago - 2 comments

#65 - Expand installation and contribution docs

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 1 comment
Labels: documentation

#64 - docs: expand about section and add to main readme

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 1 comment

#63 - Update installation tools and configuration

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 1 comment

#62 - Fix GH workflow

Pull Request - State: closed - Opened by Midnighter almost 2 years ago

#61 - Fix: handle metaphlan profiles with unclassified taxa in the lineage

Pull Request - State: closed - Opened by Midnighter almost 2 years ago - 3 comments

#60 - Feat taxonomy

Pull Request - State: closed - Opened by Midnighter almost 2 years ago

#59 - Add taxonomy to BIOM format

Issue - State: closed - Opened by Midnighter almost 2 years ago - 1 comment
Labels: enhancement

#58 - Fix bug in krakenuniq

Pull Request - State: closed - Opened by sofstam almost 2 years ago - 1 comment

#57 - Variability in KrakenUniq output causes bugs

Issue - State: closed - Opened by jfy133 almost 2 years ago

#56 - Document which column used in standarised profiles

Pull Request - State: closed - Opened by jfy133 almost 2 years ago - 1 comment

#55 - Correct document where the supported kaiju file comes from

Pull Request - State: closed - Opened by jfy133 almost 2 years ago - 1 comment