Issues

• Update summary scripts to deal with QIIME2 model changes

  bug
  HPCBio/TADA#75 · Filter by author cjfields opened on Sep 10, 2026

• Small bug with sample renaming

  bug
  HPCBio/TADA#74 · Filter by author cjfields opened on Apr 27, 2026

• Strict syntax

  HPCBio/TADA#73 · Filter by author cjfields opened on Mar 5, 2026
  1

• Switch dada inference step back to using filt instead of derep objects during pooled inference

  HPCBio/TADA#72 · Filter by author cjfields opened on Dec 4, 2025
  1

• Test Illumina cutadapt support for ITS and dovetailing primer pairs, strictness of primer matches

  HPCBio/TADA#70 · Filter by author cjfields opened on Nov 1, 2025
  1

• Adjust files to be compatible with Mia

  HPCBio/TADA#69 · Filter by author NeginValizadegan opened on Jun 11, 2025

• Skip any QC if reads are paired-end

  DSL2
  HPCBio/TADA#68 · Filter by author cjfields opened on Apr 8, 2025

• Get rid of read map file

  HPCBio/TADA#66 · Filter by author cjfields opened on Apr 4, 2025

• DADA script for quality plots doesn't work with all sequence file extensions

  HPCBio/TADA#65 · Filter by author cjfields opened on Mar 20, 2025

• Update post-DADA2 plots for quantitative details and more direct comparison to pre-QC

  DSL2enhancement
  HPCBio/TADA#64 · Filter by author cjfields opened on Feb 4, 2025

• Allow propagation of denoising info through to merging output

  DSL2good first issue
  HPCBio/TADA#63 · Filter by author cjfields opened on Feb 1, 2025

• Add back custom tax ranks

  DSL2good first issue
  HPCBio/TADA#62 · Filter by author cjfields opened on Feb 1, 2025

• Add a stop step after merging + chimera detection

  DSL2
  HPCBio/TADA#61 · Filter by author cjfields opened on Jan 29, 2025

• Screening sequences using Infernal or HMMER

  DSL2
  HPCBio/TADA#60 · Filter by author cjfields opened on Jan 26, 2025
  1

• Implement variable amplicon (ITS) subworkflow

  DSL2
  HPCBio/TADA#59 · Filter by author cjfields opened on Jan 26, 2025
  1

• Add phangorn

  DSL2
  HPCBio/TADA#57 · Filter by author cjfields opened on Jan 26, 2025

• Switch Illumina test data

  DSL2
  HPCBio/TADA#55 · Filter by author cjfields opened on Jan 14, 2025

• DECIPHER: Alignment larger than the maximum allowable size

  DSL2
  HPCBio/TADA#54 · Filter by author Charmy0619 opened on Jan 13, 2025
  4

• Refactor trimming and filtering

  DSL2
  HPCBio/TADA#49 · Filter by author cjfields opened on Oct 28, 2024
  1

• Update fluidigm-run.py to include sample sheet for PacBio

  DSL2
  HPCBio/TADA#47 · Filter by author NeginValizadegan opened on Jul 18, 2024
  1

• Address pooling when doing chimera detection

  DSL2
  HPCBio/TADA#45 · Filter by author cjfields opened on Jun 15, 2024

• Documentation cleanup

  HPCBio/TADA#40 · Filter by author cjfields opened on Jun 19, 2023
  1

• Set up Dockstore

  HPCBio/TADA#39 · Filter by author cjfields opened on Dec 22, 2022
  1

  

• Reorganizing output directories

  DSL2
  HPCBio/TADA#35 · Filter by author cjfields opened on Feb 28, 2022
  1

• Generation of large matrices and data frames takes forever

  HPCBio/TADA#34 · Filter by author cjfields opened on Feb 14, 2022
  2