bokulich-lab/q2-rgi

Issues

• CI: Error in CI setup miniconda

  #109 opened 20 hours ago
  0

• MAINT: Rename plugin to q2-rgi

  #107 opened 20 hours ago
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• MAINT: Remove everything related to AMRFinderplus

  #105 opened 2 months ago
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• REF: Create utils module.

  #100 opened 20 hours ago
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• ENH: New transformer to transform AMRFinderPlusAnnotationsDirFmt to immutable.Metadata

  #99 opened 2 months ago
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• CI: Codecov report does not show up on PRs

  #98 opened 20 hours ago
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• ENH: Adding three new parameters to run_amrfinderplus_n

  #96 opened 2 months ago
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• ENH: Change `FeatureData[AMRFinderPlusAnnotation]` type

  #94 opened 2 months ago
  0

• ENH: Add GenomeData[Proteins] and GenomeData[Loci] inputs to annotate-sample-data-amrfinderplus action

  #93 opened 2 months ago
  1

• BUG: database_format_version.txt is needed for AMRFinderplusDatabaseDirFmt

  #91 opened 4 months ago
  0

• ENH: New action that annotates `FeatureData[Sequence]` and `FeatureData[ProteinSequence]`.

  #89 opened 2 months ago
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• ENH: Action to annotate SampleData[MAGs] with amrfinderplus

  #87 opened 4 months ago
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• ENH: New type for AMRFinderPlus annotations

  #85 opened 4 months ago
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• CI: Adding new CI

  #83 opened 5 months ago
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• ENH: New type for amrfinderplus database

  #80 opened 4 months ago
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• BUG: No module named tqdm

  #78 opened 5 months ago
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• ENH: Adding new action to download NCBI database for AMRFinderPlus

  #77 opened 4 months ago
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• TEST: Coverage is low in `_formats.py` and `utils.py`

  #76 opened 7 months ago
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• CI: The name of the qiime2 distro has changed and has to be updated

  #74 opened 7 months ago
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• BUG: `sample_dict` function of `CARDAnnotationDirectoryFormat` does not include all MAGs per sample

  #72 opened 7 months ago
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• BUG: ValueError when running `collate-reads-allele-annotations`

  #69 opened 8 months ago
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• ENH: Add progress bars to downloads with `fetch-card-db` action

  #67 opened 7 months ago
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• ENH: Change how the CARD database is loaded with function `load_card`

  #65 opened 5 months ago
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• ENH: Add possibility to parallelise the `annotate_mags_card` action.

  #62 opened 8 months ago
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• ENH: Add possibility to parallelise the `annotate_reads_card` action.

  #60 opened 5 months ago
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• ENH: Add sample_dict function to classes `CARDAlleleAnnotationDirectoryFormat`, `CARDAlleleAnnotationDirectoryFormat` and `CARDAnnotationDirectoryFormat`

  #58 opened 8 months ago
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• MAINT: Change order of qiime2 channels in installation instructions.

  #57 opened 9 months ago
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• ENH: Add three actions that can collate the annotations of mags and reads for parallelization of the kmer-query functions.

  #55 opened 8 months ago
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• ENH: Add three actions that can partition the annotations of mags and reads for parallelization of the kmer-query functions.

  #53 opened 7 months ago
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• ENH: Add transformer for kmer analysis formats to Metadata

  #51 opened 7 months ago
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• MAINT: Change imports from types-genomics to types.

  #49 opened 9 months ago
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• ENH: Add new sematic types `CARDReadsKmerAnalysis` and `CARDMAGsKmerAnalysis`

  #47 opened 9 months ago
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• ENH: Add sorted.length_100.bam file to `CARDAlleleAnnotation` when running `annotate_reads_card`

  #45 opened 10 months ago
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• Adding `Genelengths` type

  #42 opened 7 months ago
  1

• ENH: Change Presence/Absence table to Frequency table in `annotate-mags-card` output

  #40 opened 10 months ago
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• BUG: Heatmap produces error becuase it does not recognise JSON files

  #37 opened 10 months ago
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• MAINT: Include second installation instructions for Apple silicone chips

  #36 opened 10 months ago
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• MAINT: Remove altair from installation instructions

  #35 opened 10 months ago
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• Tests don't run in CI, because of pyarrow dependency of Altair

  #34 opened 10 months ago
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• When running `annotate-reads-card` without the flag `--p-include-wildcard` the gene and allele mapping outputs contain the same information

  #31 opened a year ago
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• BUG: Invalid value for '--i-amr-reads-annotation' in `visualize-annotation-stats`

  #30 opened a year ago
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• `CARDGeneAnnotationDirectoryFormat` contains stats file that is not needed

  #28 opened a year ago
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• BUG: "biom.exception.TableException: Duplicate observation IDs" when running `annotate-reads-card`

  #26 opened 10 months ago
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• ENH: Add new action that can normalize `FeatureTable[Frequency]` with different methods.

  #23 opened 4 months ago
  1

• ENH: Add new q2-amr action that builds a kmer database of custom kmer lengths.

  #22 opened 5 months ago
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• ENH: Add new action that predicts the origin of detected ARGs.

  #21 opened 5 months ago
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• ENH: Add aligner property to annotate-reads-card outputs

  #19 opened 10 months ago
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• Test whether the RGI fix is still needed

  #16 opened a year ago
  1

• Re-format the code using `black`

  #15 opened a year ago
  4

• Make sure installation instructions work

  #14 opened a year ago
  1