nf-core/deepmodeloptim

Issues

• Turn torch_tune into an nf-core module

  #201 opened 2 months ago by JoseEspinosa
  0

• [enhancement] do .yaml config parsing and puting into channels in groovy instead of python

  #205 opened a month ago by mathysgrapotte
  0

• Turn stimulus_analysis_default into an nf-core module

  #198 opened 2 months ago by JoseEspinosa
  0

• Turn stimulus_split_csv into an nf-core module

  #199 opened 2 months ago by JoseEspinosa
  0

• Move datasets into nf-core/testdata

  #204 opened a month ago by luisas
  1

• Move test data to the nf-core test dataset repo

  #184 opened 2 months ago by JoseEspinosa
  0

• Add meta to the pipeline

  #203 opened a month ago by luisas
  0

• Freeze the stimulus container to seqera wave

  #202 opened a month ago by mathysgrapotte
  0

• Turn stimulus_transform_csv into an nf-core module

  #200 opened 2 months ago by JoseEspinosa
  0

• Turn check_torch_model into an nf-core module

  #197 opened 2 months ago by JoseEspinosa
  0

• [future][discussion] how to incorporate external modules ?

  #195 opened 2 months ago by mathysgrapotte
  0

• Turn the following modules into nf-core modules

  #194 opened 2 months ago by mathysgrapotte
  0

• Collect local module versions

  #189 opened 2 months ago by JoseEspinosa
  1

• Adapt modules to the nf-core structure

  #191 opened 2 months ago by JoseEspinosa
  1

• [future][discussion] deal with data located in files

  #196 opened 2 months ago by mathysgrapotte
  0

• [feat] have test data in a different repo

  #146 opened 2 months ago by luisas
  2

• Fix nf-test after nf-core migration

  #193 opened 2 months ago by JoseEspinosa
  0

• Adapt subworkflow to the nf-core structure

  #192 opened 2 months ago by JoseEspinosa
  0

• Adapt components to the nf-core structure

  #190 opened 2 months ago by JoseEspinosa
  0

• Reconciliate the previous readme with nf-core one

  #185 opened 2 months ago by JoseEspinosa
  0

• Update test_full.config

  #188 opened 2 months ago by JoseEspinosa
  0

• Implement nf-core full tests

  #186 opened 2 months ago by JoseEspinosa
  0

• Add a real test data set for full testing

  #187 opened 2 months ago by JoseEspinosa
  0

• [feat] outsource python package to a different repo ready for pip deployment

  #179 opened 2 months ago by mathysgrapotte
  1

• [feat] add a check on split parameters values.

  #151 opened 2 months ago by alessiovignoli
  1

• ray init does not automaticly detect GPUs

  #157 opened 6 months ago by alessiovignoli
  1

• [analysis] provide a report of auc vs data modification

  #136 opened 2 months ago by suzannejin
  1

• [feat] add an early stopper for ray tune

  #142 opened 2 months ago by suzannejin
  2

• [feat] resume ray tune

  #144 opened 2 months ago by suzannejin
  1

• Performance: define metrics per class

  #147 opened 2 months ago by luisas
  1

• [bug] If there is only one metric, analysis step crashes

  #148 opened 2 months ago by luisas
  1

• [feat] robust way of defining and importing the model class

  #158 opened 2 months ago by suzannejin
  1

• [feat] GaussianChunk to nf-test handle_data.nf.test

  #165 opened 2 months ago by alessiovignoli
  1

• [feat] python module to validate the tune config fields.

  #167 opened 2 months ago by alessiovignoli
  2

• [feat] parallelize predict wrapper

  #178 opened 2 months ago by suzannejin
  3

• [feat] add a way to assess the impact of different initial weights on the learning

  #171 opened 2 months ago by suzannejin
  1

• [feat] experiment conf json "custom" section should provide a slot "name" for the naming of each configuration

  #176 opened 2 months ago by suzannejin
  1

• [feat] analysis default should provide figures about the prediction values

  #175 opened 2 months ago by suzannejin
  1

• retraining models with stimulus with pulling from checkpoints (all models degrade overtime)

  #181 opened 2 months ago by mathysgrapotte
  0

• [feat] create a nf-core pipeline config for the pipeline

  #180 opened 3 months ago by JoseEspinosa
  0

• [bug] multiprocessing doesn't work in ikernels

  #173 opened 3 months ago by mathysgrapotte
  1

• [fix] ray tune runs forever sometimes

  #143 opened 5 months ago by suzannejin
  3

• [feat] force raytune to have maximum running time

  #159 opened 5 months ago by suzannejin
  1

• [feat] custom function for tune to sample x number from space

  #160 opened 5 months ago by suzannejin
  0

• [fix] the output of the forward step should be tensor, never dict

  #137 opened 7 months ago by suzannejin
  0

• [fix] we want to transform the entire data

  #139 opened 7 months ago by suzannejin
  0

• [feature] add logging functionalities

  #138 opened 7 months ago by mathysgrapotte
  0

• [seqera platform] on seqera platform, pipeline crashes since it is allowed just 1.GB of memory by default

  #155 opened 4 months ago by mathysgrapotte
  1

• Make pipeline run on GPU (+checks)

  #149 opened 6 months ago by luisas
  1

• Add `ps` to all containers

  #141 opened 7 months ago by evanfloden
  2