aomlomics/tourmaline

Issues

• Delete any mention of evenness_group_significance.qzv in pseudorules and report

  #138 opened 2 months ago by lukenoaa
  1

• Create taxonomy notebook to make taxonomy stacked bar charts and treemap charts

  #139 opened 2 months ago by lukenoaa
  1

• Generate taxonomy information that is separated by taxonomic rank

  #113 opened a year ago by ksilnoaa
  1

• Create single stats file for sample step

  #137 opened 3 months ago by ksilnoaa
  0

• Update fastqc_per_base_sequence_quality_dropoff.py

  #135 opened 3 months ago by ksilnoaa
  2

• Include script to demultiplex raw reads by sample barcodes and marker

  #136 opened 3 months ago by ksilnoaa
  0

• Create table of number of reads retained per sample at each step

  #128 opened 3 months ago by lukenoaa
  3

• Tourmaline initial set-up in v2

  #134 opened 3 months ago by ksilnoaa
  1

• Upload curated versions of reference databases to Zenodo

  #92 opened 3 months ago by lukenoaa
  2

• Syntax warning for invalid escape sequences

  #121 opened 3 months ago by lukenoaa
  0

• Stop using distplot in Python notebook

  #130 opened 3 months ago by lukenoaa
  0

• Typo in Python notebook

  #129 opened 3 months ago by lukenoaa
  0

• config.yaml updates

  #122 opened 3 months ago by lukenoaa
  0

• Delete _config.yaml (not being used)

  #120 opened 3 months ago by lukenoaa
  0

• Installing multiqc with Rosetta running

  #127 opened 4 months ago by lukenoaa
  0

• User-provided file path for reference database/classifier

  #126 opened 5 months ago by lukenoaa
  0

• Tourmaline 2.0 mega-issue

  #125 opened 5 months ago by lukenoaa
  0

• Add rescript qiime plugin to Tourmaline Docker

  #124 opened 6 months ago by ksilnoaa
  0

• Check for metadata beta_group_column prior to diversity step, not at beginning

  #123 opened 6 months ago by ksilnoaa
  0

• Check comments/instructions about filtering

  #119 opened 7 months ago by lukenoaa
  0

• Documentation updates

  #118 opened 8 months ago by lukenoaa
  0

• rule check_inputs_params_se: missing param

  #117 opened 8 months ago by rckarns8
  1

• Add code guidance to export outputs to phyloseq

  #116 opened a year ago by ksilnoaa
  0

• Make the diversity step optional

  #115 opened a year ago by ksilnoaa
  0

• Update qiime2 osx/linux install instructions

  #114 opened a year ago by ksilnoaa
  0

• Relate config file with AOML-MIMARKS metadata terms

  #112 opened a year ago by ksilnoaa
  0

• Add rule to prepare output format for uploading to DwC

  #103 opened a year ago by ksilnoaa
  1

• Export BIOM table (.tsv) plus taxonomy

  #89 opened a year ago by lukenoaa
  3

• Update init from existing repo script

  #111 opened a year ago by ksilnoaa
  0

• Add new version to docker hub

  #105 opened a year ago by ksilnoaa
  0

• Install all R packages through conda

  #99 opened a year ago by lukenoaa
  2

• qiime not successfully installed (Linux)

  #104 opened a year ago by BCArg
  1

• Report: record database version

  #88 opened a year ago by lukenoaa
  2

• Add snakemake rule to filter out samples

  #84 opened a year ago by ksilnoaa
  2

• Workflow is failing at diversity step for some users

  #80 opened a year ago by lukenoaa
  10

• ILP solver warning on Qiime2-2023.2 branch when installed from yaml

  #101 opened a year ago by ksilnoaa
  1

• Report: add how taxonomy was generated

  #91 opened 2 years ago by lukenoaa
  2

• Provide conda environments as YAML files

  #86 opened 2 years ago by lukenoaa
  1

• Add utility scrips to check that primers/adapters removed

  #90 opened 2 years ago by lukenoaa
  2

• Graphviz not installed, so DAG command won't work

  #100 opened a year ago by ksilnoaa
  1

• Snakemake is re-running denoising when using filtered commands

  #98 opened a year ago by lukenoaa
  3

• Travis, dependencies, and continuous integration tests (not unit tests)

  #93 opened 2 years ago by lukenoaa
  0

• Create Singularity container

  #87 opened 2 years ago by lukenoaa
  0

• Versioning to allow for new versions (major/minor updates)

  #85 opened 2 years ago by lukenoaa
  0

• Feature metadata: Add Genbank best hit (MegaBLAST vs. nt)

  #96 opened 2 years ago by lukenoaa
  0

• Feature metadata: add percent GC

  #95 opened 2 years ago by lukenoaa
  0

• Add support for fragment insertion tree

  #94 opened 2 years ago by lukenoaa
  0

• Calculate MD5 checksums of sequences and compare to DADA2/Deblur seqids

  #97 opened 2 years ago by lukenoaa
  0

• issues running with test dataset

  #82 opened 2 years ago by LennWhy
  2

• building with Qiime2-2022.2 py38 fails on dependencies

  #78 opened 2 years ago by splaisan
  2