sequana/sequana_pipetools

Issues

• remove deprecated functions

  #84 opened a year ago by cokelaer
  0

• would be nice to have a mechanism to get the choices from a schema file to use within the manager

  #88 opened a year ago by cokelaer
  1

• thorough update of the README / documentation

  #99 opened a year ago by cokelaer
  0

• Finalise slurm status with nicer layout/info

  #80 opened a year ago by cokelaer
  0

• should look for slurm files in the logs using glob

  #86 opened a year ago by cokelaer
  0

• multiqc_config and schema.yaml in the working directory should also be soft links

  #85 opened a year ago by cokelaer
  0

• --from-project need to redefined with the new click setup

  #90 opened a year ago by cokelaer
  1

• deprecated/useless functions

  #91 opened a year ago by cokelaer
  1

• sort alphabetically the different click options

  #87 opened a year ago by cokelaer
  1

• sequana version not stored in info.txt

  #89 opened a year ago by cokelaer
  0

• remove/deprecate cluster_config in favor of profile

  #79 opened a year ago by cokelaer
  0

• Uses profile

  #81 opened a year ago by cokelaer
  0

• conversion argparse to click

  #76 opened a year ago by cokelaer
  0

• if long item/key are provided when filling the yaml, lines have unexpected return carriage

  #77 opened a year ago by cokelaer
  1

• download using aiohttp fails on python 3.9 with too many requests error

  #61 opened a year ago by cokelaer
  0

• Use versionix to get versions of requirements automatically

  #68 opened a year ago by cokelaer
  0

• PipelineManagerDirectory should populate the wrapper version like PipelineManager

  #64 opened a year ago by cokelaer
  0

• automatically fetch wrapper version from the config file

  #62 opened a year ago by cokelaer
  0

• use APPTAINER_BINDPATH

  #53 opened 2 years ago by cokelaer
  1

• when not setting --prefix-apptainer, shell script does not set prefix properly

  #49 opened 2 years ago by cokelaer
  0

• add --use-apptainer instead of --use-singularity

  #45 opened 2 years ago by cokelaer
  0

• update get_statistitcs with wrapper instead of rules

  #40 opened 2 years ago by cokelaer
  0

• remove dynamic rule function

  #39 opened 2 years ago by cokelaer
  0

• should be able to handle data with no read tag (assuming single end)

  #37 opened 2 years ago by cokelaer
  0

• Handle slurm directory to use `--profile`

  #35 opened 2 years ago by ddesvillechabrol
  0

• Simplify the setup() method to remove globals() need

  #29 opened 3 years ago by cokelaer
  0

• update onerror section

  #1 opened 3 years ago by cokelaer
  1