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44 Open 47 Closed
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Issues list

Remove unnecessary sample_id values in input channels enhancement New feature or request nice to have Stretch goal if time quick-fix Low-hanging fruit
#122 opened May 24, 2024 by lina-kim
Give user option to split pre-denoised samples by name/accession instead of number core-function Related to core functionality nice to have Stretch goal if time
#121 opened Apr 27, 2024 by lina-kim
@lina-kim
Set up static GitHub Pages-based documentation testing Improvements or additions to testing
#120 opened Apr 23, 2024 by lina-kim Beta release 1.0b 🪄
@lina-kim
Configure different parameter sets for ITS-based Cutadapt runs
#119 opened Apr 23, 2024 by lina-kim ITS configuration 🍄
Add iterative Cutadapt runs for ITS
#118 opened Apr 23, 2024 by lina-kim ITS configuration 🍄
Make feature classification step optional enhancement New feature or request quick-fix Low-hanging fruit
#117 opened Apr 19, 2024 by lina-kim
Set up workflow profiles for execution on local, slurm, parallel, etc.
#116 opened Apr 9, 2024 by lina-kim
Run CHECK_FASTQ_TYPE() in parallel with trimming/denoising, not through
#115 opened Apr 9, 2024 by lina-kim
Incorporate input metadata table into visualizations e.g. taxa barplot enhancement New feature or request nice to have Stretch goal if time
#113 opened Apr 4, 2024 by lina-kim
Make taxonomy-based collapse optional enhancement New feature or request quick-fix Low-hanging fruit
#107 opened Mar 14, 2024 by lina-kim
Suggest users use local versions of reference files/databases instead of hardcoding wget links
#104 opened Mar 4, 2024 by lina-kim
Allow detection of pre-trimmed samples bug Something isn't working
#86 opened Dec 13, 2023 by lina-kim
Improve accuracy of taxonomic classification using full-length reference sequences analysis-needed Less implementation, more analysis enhancement New feature or request
#85 opened Dec 11, 2023 by lina-kim
Add automated rarefaction and/or user-input parameters core-function Related to core functionality enhancement New feature or request nice to have Stretch goal if time
#84 opened Dec 6, 2023 by lina-kim
@lina-kim
1
Build environments specific to osx-arm64 machines enhancement New feature or request
#81 opened Nov 29, 2023 by lina-kim
Nicely integrate q2-fondue with automated Conda or Docker-based executions core-function Related to core functionality
#75 opened Nov 17, 2023 by lina-kim Beta release 1.0b 🪄
@lina-kim
1
Clean up documentation for initial release core-function Related to core functionality
#73 opened Nov 10, 2023 by lina-kim Beta release 1.0b 🪄
@lina-kim
Clean up references using Nextflow input repeaters enhancement New feature or request quick-fix Low-hanging fruit
#71 opened Nov 10, 2023 by lina-kim
Incorporate anywhere/adapter-based Cutadapt primer removal enhancement New feature or request nice to have Stretch goal if time quick-fix Low-hanging fruit
#70 opened Nov 10, 2023 by lina-kim
1
Wrap Nextflow workflow into QIIME 2 plugin core-function Related to core functionality
#69 opened Nov 9, 2023 by lina-kim
@ChristosMatzoros
Calculate phylogenetic core metrics core-function Related to core functionality
#65 opened Nov 1, 2023 by lina-kim
Filter tables after taxonomy classification to remove non-target sequences / contaminants / macrofungi analysis-needed Less implementation, more analysis enhancement New feature or request
#64 opened Nov 1, 2023 by lina-kim
Expose all user-input FastQC parameters to user quick-fix Low-hanging fruit
#61 opened Jun 8, 2023 by lina-kim
Expose mutually exclusive parameters in Cutadapt to user enhancement New feature or request quick-fix Low-hanging fruit
#60 opened Jun 7, 2023 by lina-kim
Automate identification of primers within samples enhancement New feature or request nice to have Stretch goal if time
#59 opened Jun 2, 2023 by lina-kim
ProTip! no:milestone will show everything without a milestone.