SATAY-LL/Transposonmapper

Issues

• Run the Benoit R code with their data and our data and do a replication study

  #79 opened 2 years ago by leilaicruz
  1

• Discard the maximum read from the postprocessing script Transposonmapper

  #76 opened 3 years ago by leilaicruz
  0

• Add preprocessing steps to the JupyterBook documentation and Readme file

  #74 opened 3 years ago by leilaicruz
  0

• Include DpnII and NlaIII digestion site trimming

  #73 opened 3 years ago by EKingma
  5

• Update save_as_wig.py

  #69 opened 3 years ago by leilaicruz
  3

• Update the docker image with updates on the analysis packages

  #72 opened 3 years ago by leilaicruz
  0

• Post processing functions require pysam

  #64 opened 3 years ago by T-Wisse
  7

• Add a FIX for volcano plots

  #62 opened 3 years ago by leilaicruz
  1

• Workshop troubleshooting

  #60 opened 3 years ago by leilaicruz
  4

• Workshop

  #40 opened 3 years ago by leilaicruz
  4

• Write (draft) software maintenance document

  #61 opened 3 years ago by mwakok
  0

• GitHub Action for Docker push

  #41 opened 3 years ago by mwakok
  4

• Reorganize Juptyerbook content

  #51 opened 3 years ago by mwakok
  5

• Archive Jupyterbook repository

  #59 opened 3 years ago by mwakok
  0

• Upload Docker image to DockerHub

  #4 opened 3 years ago by mwakok
  2

• add a github action workflow for the publishing of the jupyter Book

  #52 opened 3 years ago by leilaicruz
  2

• Upload package to PyPI

  #5 opened 3 years ago by mwakok
  2

• Release_v1.1.0

  #56 opened 3 years ago by mwakok
  4

• Update GUI for Docker use

  #3 opened 3 years ago by mwakok
  1

• Image upload

  #22 opened 3 years ago by mwakok
  1

• Add bump2version support

  #50 opened 3 years ago by mwakok
  1

• Adding a button in the GUI that redirects to the documentation website

  #45 opened 3 years ago by leilaicruz
  5

• Create Contributing file

  #24 opened 3 years ago by mwakok
  0

• Export and visualizing coverage reports upon pushing

  #7 opened 3 years ago by leilaicruz
  0

• Discuss documentation methods

  #6 opened 3 years ago by mwakok
  0

• Update legacy documentation in code

  #2 opened 3 years ago by mwakok
  0

• Update Link to Zenodo

  #1 opened 3 years ago by mwakok
  9

• Update contents documentation folder

  #49 opened 3 years ago by mwakok
  2

• Register software in PURE

  #28 opened 3 years ago by mwakok
  1

• the CITATION.cff file cannot be parsed

  #42 opened 3 years ago by leilaicruz
  1

• Tasks for each python script to design unit tests

  #18 opened 3 years ago by leilaicruz
  2

• Integration with SonarCloud for coverage reports

  #39 opened 3 years ago by leilaicruz
  0

• Not accepting relative paths during run on the local docker container

  #31 opened 3 years ago by leilaicruz
  4

• Move the wiki from the old repo to this one

  #35 opened 3 years ago by leilaicruz
  1

• Look into use of containerization

  #8 opened 3 years ago by mwakok
  5

• Overview test environment

  #19 opened 3 years ago by mwakok
  0

• Improve organisation code base

  #23 opened 3 years ago by mwakok
  0

• Improve branch management (GitFlow)

  #21 opened 3 years ago by mwakok
  2

• Develop repoducible analysis pipeline

  #20 opened 3 years ago by mwakok
  0

• Use conda environments to manage dependencies

  #17 opened 3 years ago by mwakok
  2

• Write down all tasks of each python script

  #16 opened 3 years ago by mwakok
  1

• Update LICENSE

  #15 opened 3 years ago by mwakok
  3

• Improve modularity of code base

  #14 opened 3 years ago by mwakok
  0

• Create Code of Conduct

  #13 opened 3 years ago by mwakok
  0

• Create first integration test

  #12 opened 3 years ago by mwakok
  0

• Putting the docker document for users from the wiki to the JupyterBook

  #11 opened 3 years ago by leilaicruz
  0

• Create Citation file

  #10 opened 3 years ago by mwakok
  1

• Create zenodo.json file

  #9 opened 3 years ago by mwakok
  0