oda-hub/nb2workflow

Issues

• [Galaxy] Exception if output is not annotated

  #194 opened 2 months ago by dsavchenko
  1

• why input is changing ">" to "__gt__"?

  #196 opened 2 months ago by volodymyrss
  0

• Cell timeout (presumably due to the large output)

  #157 opened 7 months ago by dsavchenko
  6

• add parameter description annotation

  #161 opened 3 months ago by volodymyrss
  1

• nb2workflow optional parameters

  #191 opened 3 months ago by volodymyrss
  0

• Please revert back my unwanted push

  #188 opened 4 months ago by ferrigno
  1

• Typo in annotation may lead to type check error

  #186 opened 4 months ago by dsavchenko
  0

• make a way to restrict access to some groups

  #185 opened 5 months ago by volodymyrss
  0

• Backend container don't start with volume provisioned through NFS

  #182 opened 5 months ago by dsavchenko
  6

• '=' in string parameter produces issues

  #181 opened 5 months ago by dsavchenko
  0

• Properly treat the case if parameter default is None (but it's annotated)

  #136 opened 5 months ago by dsavchenko
  4

• Really need to support multiline parameter definitions

  #153 opened 5 months ago by dsavchenko
  0

• make configurable ephemeral storage and other resources

  #176 opened 5 months ago by volodymyrss
  1

• "Unknown owl type uri http://odahub.io/ontology#String. Creating basic Parameter object."

  #177 opened 5 months ago by volodymyrss
  0

• notebooks should have access to requesters oda token

  #158 opened 5 months ago by volodymyrss
  2

• in deploy: check temp dir name to be compatible with RFC 1123

  #108 opened 5 months ago by dsavchenko
  0

• learn how to generate .shed.yaml

  #125 opened 5 months ago by volodymyrss
  0

• ensure galaxy tool id contains only valid characters

  #130 opened 5 months ago by dsavchenko
  0

• make an annotation to use claim file as external data resource

  #163 opened 6 months ago by volodymyrss
  0

• check size of the file before download

  #156 opened 6 months ago by volodymyrss
  2

• clean old run directories

  #169 opened 6 months ago by volodymyrss
  0

• make an annotation to remote archive

  #154 opened 7 months ago by volodymyrss
  0

• add resource constrains, memory and CPU

  #160 opened 7 months ago by volodymyrss
  0

• add annotation for requesting local database

  #110 opened 7 months ago by volodymyrss
  0

• binary product issue

  #159 opened 7 months ago by volodymyrss
  0

• add support for annotations of workflow access to resource (storage and compute)

  #138 opened 8 months ago by volodymyrss
  1

• support pip inside tool as a demonstrator

  #152 opened 8 months ago by volodymyrss
  2

• from html remove cell with output glueing

  #146 opened 8 months ago by volodymyrss
  0

• if we have input parameter of type POSIXPath annotation and it is a URL (http://...) it needs be downloaded before running

  #139 opened 8 months ago by volodymyrss
  0

• `ruamel.yaml` dependency conflict

  #137 opened 8 months ago by burnout87
  8

• incompatibility with `Flask==3.0.2`

  #143 opened 8 months ago by burnout87
  0

• nb2galaxy: help text as CDATA without encoding symbols

  #145 opened 8 months ago by dsavchenko
  0

• Add annotation for high memory requirement

  #142 opened 8 months ago by volodymyrss
  0

• cleanup fails in case of exception in nbadapter.py:429

  #116 opened 9 months ago by okolo
  0

• Send callback upon job start

  #134 opened 9 months ago by dsavchenko
  1

• test_callback code cleanup

  #132 opened 10 months ago by okolo
  0

• Running long tasks on MMODA

  #111 opened 10 months ago by dsavchenko
  7

• return jobdir while job is still not done

  #129 opened 10 months ago by volodymyrss
  0

• treat file url parameter type

  #128 opened 10 months ago by volodymyrss
  0

• how to make large annotations

  #127 opened a year ago by volodymyrss
  0

• Logging from nb2workflow

  #120 opened a year ago by burnout87
  2

• think how to run mmoda nb tests

  #124 opened a year ago by volodymyrss
  0

• add tests by saving default output with planemo --update_test_data

  #123 opened a year ago by volodymyrss
  0

• support passing structured objects, represented by arbitrary json

  #118 opened a year ago by volodymyrss
  0

• running nb2workflow fails on python 3.12

  #113 opened a year ago by okolo
  4

• try to reduce overhead

  #109 opened a year ago by volodymyrss
  0

• Add build-essential in the nb2deploy container

  #99 opened a year ago by dsavchenko
  0

• Inconsistent behavior between sync and async when request contains unknown argument

  #98 opened a year ago by dsavchenko
  0

• Automatically wrap some outputs as oda_api product

  #97 opened a year ago by dsavchenko
  0

• it should be also allowed to run job container from service

  #95 opened a year ago by volodymyrss
  0