ctmrbio/stag-mwc

Issues

• Error in Bowtie2 and kraken2 db

  #221 opened 10 months ago by mksherwani
  2

• Include text file summarizing versions of all tools used, database versions, and StaG verison

  #218 opened a year ago by boulund
  0

• Generalize metaphlan heatmap plotting script to also handle Kaiju and Kraken2 results

  #144 opened a year ago by boulund
  1

• Update AMR++ to v3

  #199 opened a year ago by boulund
  1

• New assembly+binning workflow

  #207 opened a year ago by boulund
  1

• Make HUMAnN rules use resources.tmpdir directive instead of params.tmpdir

  #213 opened a year ago by boulund
  1

• KrakenUniq does not work when skipping host removal (host_removal: False)

  #210 opened a year ago by boulund
  1

• KrakenUniq not working with Singularity

  #198 opened a year ago by boulund
  1

• Remove str conversions in all rules

  #125 opened 5 years ago by boulund
  2

• kreport2krona.py fails on candidate taxa

  #171 opened a year ago by luhugerth
  3

• Include unclassified in mpa_style output from kraken2 and krakenuniq

  #174 opened 3 years ago by boulund
  0

• KrakenUniq module: add Krona, mpa-style output, area plot

  #191 opened a year ago by boulund
  1

• Add feature to disable metaphlan heatmap plot

  #201 opened a year ago by boulund
  1

• Make StaG-mwc Snakemake workflow standards compliant

  #186 opened a year ago by boulund
  3

• Add rule to automatically download test data

  #195 opened a year ago by boulund
  2

• Bump minimum required Snakemake version

  #189 opened a year ago by boulund
  1

• Amount of CPUs/threads for rules running in Slurm is incorrect

  #202 opened a year ago by boulund
  1

• Cannot generate report with --use-singularity

  #193 opened 2 years ago by boulund
  1

• Remove outdated DB download rules

  #187 opened 2 years ago by boulund
  0

• Fix broken reference to StaG logo in reports

  #185 opened 2 years ago by boulund
  1

• make krona plots optional

  #184 opened 2 years ago by luhugerth
  2

• Replace Bowtie2 wrapper with proper bowtie2 call; bowtie2 won't work with --use-singularity

  #152 opened 3 years ago by boulund
  1

• keep_kreport broken in host_removal

  #178 opened 3 years ago by boulund
  1

• Change container build service from singularity hub

  #169 opened 3 years ago by boulund
  4

• preprocessing_read_counts is confused about host DNA

  #172 opened 3 years ago by luhugerth
  2

• Check for metaphlan db paths when running humann

  #170 opened 3 years ago by boulund
  0

• Figure out a better way to present identified SAMPLES to the user

  #129 opened 3 years ago by boulund
  3

• BioBakery update (MetaPhlAn3, StrainPhlAn3, HUMAnN3)

  #158 opened 3 years ago by AroArz
  11

• Update HUMAnN2 to recent version compatible with MetaPhlAn2 output

  #138 opened 3 years ago by boulund
  4

• scripts/preprocessing_summary.py parsing wrong info?

  #164 opened 3 years ago by boulund
  2

• bracken2krona rule is broken

  #167 opened 3 years ago by kcivkulis
  7

• preprocessing_summary error

  #163 opened 4 years ago by AroArz
  3

• Replace GROOT

  #120 opened 4 years ago by boulund
  1

• Crash during report generation when running with Singularity

  #160 opened 4 years ago by boulund
  8

• Module docs intro paragraph is out of date

  #151 opened 5 years ago by boulund
  0

• Slurm jobs don't request threads as defined in slurm profile

  #153 opened 5 years ago by boulund
  0

• Report: all_samples.kraken2.mpa_style.txt description text requires editing

  #148 opened 5 years ago by boulund
  0

• Preprocessing read counts pdf legend is all over the place

  #149 opened 5 years ago by boulund
  1

• Report: Bracken and Filtered Bracken output tables have the same description text

  #147 opened 5 years ago by boulund
  0

• Create diagnostics plot: barplot of tax composition of filtered Bracken table

  #119 opened 5 years ago by boulund
  6

• Put citations inside report instead of just printing to stdout after finishing run

  #131 opened 5 years ago by boulund
  1

• Add Krona plots for Bracken and filtered Bracken output

  #128 opened 5 years ago by boulund
  2

• Replace BBMap host removal with Kraken2 dito

  #142 opened 5 years ago by boulund
  0

• Make it possible to shortcut early steps

  #118 opened 5 years ago by boulund
  5

• Unified output table format for taxonomic profilers

  #132 opened 5 years ago by boulund
  1

• Add Bracken

  #117 opened 5 years ago by boulund
  0

• Plot proportion host as a barplot of all samples in addition to histogram.

  #127 opened 5 years ago by boulund
  1

• Kraken2 confidence level

  #123 opened 5 years ago by boulund
  1

• Review and improve output folder names

  #122 opened 5 years ago by boulund
  2

• Configfile: remove_human is always True

  #121 opened 5 years ago by boulund
  1