segrelab/MiCoNE

Issues

• Fix julia paths for flashweave environment

  #205 opened 2 years ago by dileep-kishore
  0

• Use same settings for single and paired end alternatives

  #206 opened 2 years ago by dileep-kishore
  0

• FileNotFoundError: [Errno 2] No such file or directory: '/home/datb/miniconda3/envs/micone/lib/python3.8/site-packages/micone/config/configs/datatypes.toml'

  #208 opened 2 years ago by papelypluma
  1

• Use conda Python api in micone --init

  #204 opened 2 years ago by dileep-kishore
  0

• NetCoMi installation fails

  #203 opened 2 years ago by dileep-kishore
  0

• UTF-8 bug in qiime2 modules when running in nextflow under qsub

  #178 opened 2 years ago by dileep-kishore
  1

• Create a conda recipe for micone

  #194 opened 2 years ago by dileep-kishore
  0

• Fix the gg qiime2 classifier artifact

  #154 opened 2 years ago by dileep-kishore
  1

• Fix the SILVA classifier artifact

  #159 opened 2 years ago by dileep-kishore
  0

• Create a log parser to parse select information from mindpipe log files

  #166 opened 2 years ago by dileep-kishore
  0

• Create a `utils` submodule that creates the `config` file programatically

  #197 opened 3 years ago by dileep-kishore
  1

• Display all errors at end of run (like pytest)

  #202 opened 3 years ago by dileep-kishore
  1

• Stop all subprocesses when there is an error during a run

  #156 opened 3 years ago by dileep-kishore
  2

• Migrate to nextflow DSL 2 workflows

  #189 opened 3 years ago by dileep-kishore
  0

• Allow support for process aliases in `config.toml` file

  #201 opened 3 years ago by dileep-kishore
  2

• Replace `otu_assignment` with `denoise_cluster` in config

  #182 opened 4 years ago by dileep-kishore
  0

• Add project description to pypi deployment

  #193 opened 4 years ago by dileep-kishore
  0

• Create a method to add/combine two `NetworkGroup` objects

  #200 opened 4 years ago by dileep-kishore
  0

• Update `make_network` module to support excluding p-values

  #198 opened 4 years ago by dileep-kishore
  1

• Add module for network inference using FlashWeave.jl

  #199 opened 4 years ago by dileep-kishore
  1

• Add module for network inference using SPRING

  #196 opened 4 years ago by dileep-kishore
  2

• Update the README

  #192 opened 4 years ago by dileep-kishore
  0

• Remove pin on jedi and parso dependencies once ipython issue is fixed

  #190 opened 4 years ago by dileep-kishore
  0

• Recreate entry points after migration to pyproject.toml

  #195 opened 4 years ago by dileep-kishore
  0

• Fix schematics and validate methods

  #191 opened 4 years ago by dileep-kishore
  1

• Should we draw the pipline workflow without graphviz and pygraphviz [#j7049g]

  #188 opened 4 years ago by dileep-kishore
  2

• Move to github workflows

  #187 opened 4 years ago by dileep-kishore
  1

• Construct module to calculate consensus network

  #177 opened 4 years ago by dileep-kishore
  1

• Implement `clean` subcommand

  #155 opened 6 years ago by dileep-kishore
  0

• Bugs in the pipeline CLI

  #172 opened 6 years ago by dileep-kishore
  0

• Switch off spinners for non-interactive runs

  #176 opened 6 years ago by dileep-kishore
  0

• Fix sparcc environment specification

  #175 opened 6 years ago by dileep-kishore
  0

• Check environment initialization only for processes in current run

  #167 opened 6 years ago by dileep-kishore
  0

• Save pipeline

  #173 opened 6 years ago by dileep-kishore
  1

• Fix mLDM environment

  #174 opened 6 years ago by dileep-kishore
  0

• Fix bug in pipenv dependency resolution

  #171 opened 6 years ago by dileep-kishore
  0

• Current network datastructures do not support multiple edges

  #169 opened 6 years ago by dileep-kishore
  1

• Bug in `NetworkGroup._combine_methods`

  #170 opened 6 years ago by dileep-kishore
  1

• Make Network load big datasets faster

  #168 opened 6 years ago by dileep-kishore
  2

• Use fdr instead of bh for pvalue correction

  #165 opened 6 years ago by dileep-kishore
  1

• Factor out the resampling and pvalue calculation step out of sparcc pipeline and into separate pipelines

  #164 opened 6 years ago by dileep-kishore
  0

• Support for parameterization of process using 4 level process name

  #162 opened 6 years ago by dileep-kishore
  0

• Pipeline does not wait for last process

  #161 opened 6 years ago by dileep-kishore
  0

• Remove "_filtered" suffix from abundance filter pipeline

  #160 opened 6 years ago by dileep-kishore
  0

• Pipeline does not wait after resume

  #163 opened 6 years ago by dileep-kishore
  0

• Higher level network file shows full lineage upto species level

  #158 opened 6 years ago by dileep-kishore
  0

• Attaching inputs to outputs must have > 1 level recursion

  #157 opened 6 years ago by dileep-kishore
  0

• Script and config files should have unique names

  #153 opened 6 years ago by dileep-kishore
  0

• `Params.copy` does not seem to copy location

  #152 opened 6 years ago by dileep-kishore
  1

• Change output location (name) of process when there are multiple in pipeline

  #151 opened 6 years ago by dileep-kishore
  1