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42 Open 39 Closed
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Issues list

Check metadata file at beginning of repseqs and taxonomy
#161 opened Dec 13, 2024 by ksilnoaa
Add guidance for dereplicating reference databases for ML classifiers to docs Version 2
#160 opened Dec 2, 2024 by ksilnoaa
Add otu_db_doi and otu_db_filename to analysisMetadata
#159 opened Nov 27, 2024 by ksilnoaa
Carriage returns in asv_taxa_features.tsv Version 2
#158 opened Nov 25, 2024 by ksilnoaa
dada_stats not printing in a filtered run V1
#156 opened Nov 7, 2024 by ksilnoaa
Print out details on samples that are filtered out by dada2 Version 2
#155 opened Oct 31, 2024 by ksilnoaa
@ksilnoaa
Add functionality for Tronko taxa assignment Version 2
#154 opened Sep 24, 2024 by ksilnoaa
Incorporate filtering capabilities to V2 Version 2
#153 opened Sep 18, 2024 by ksilnoaa
How to prevent Snakemake from re-running rules when their output is already present
#152 opened Sep 18, 2024 by lukenoaa
Write script to iterate through parameters and do multiple Tourmaline runs
#151 opened Sep 13, 2024 by ksilnoaa
Write rules for dada2 SE and deblur
#149 opened Sep 13, 2024 by ksilnoaa
Test Jupyter notebooks with current Tourmaline notebook, updated package commands
#142 opened Aug 13, 2024 by ksilnoaa
1
Create single stats file for sample step
#137 opened Jul 8, 2024 by ksilnoaa
Include script to demultiplex raw reads by sample barcodes and marker
#136 opened Jul 8, 2024 by ksilnoaa
Update fastqc_per_base_sequence_quality_dropoff.py Version 2
#135 opened Jul 8, 2024 by ksilnoaa
2
Tourmaline initial set-up in v2
#134 opened Jul 1, 2024 by ksilnoaa
1
Installing multiqc with Rosetta running
#127 opened Jun 16, 2024 by lukenoaa
User-provided file path for reference database/classifier
#126 opened Apr 26, 2024 by lukenoaa
1
Tourmaline 2.0 mega-issue
#125 opened Apr 23, 2024 by lukenoaa
Add rescript qiime plugin to Tourmaline Docker
#124 opened Apr 11, 2024 by ksilnoaa
Check for metadata beta_group_column prior to diversity step, not at beginning
#123 opened Mar 26, 2024 by ksilnoaa
Check comments/instructions about filtering
#119 opened Mar 5, 2024 by lukenoaa
Documentation updates
#118 opened Feb 5, 2024 by lukenoaa
Add code guidance to export outputs to phyloseq
#116 opened Nov 15, 2023 by ksilnoaa
Make the diversity step optional enhancement New feature or request
#115 opened Nov 15, 2023 by ksilnoaa
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