Skip to main content

A workflow assembler for genome analytics and informatics

Project description

kronos is a software tool for automating reproducible, auditable and distributable bioinformatics workflow development. It obviates explicit coding for workflow development to a great extent by compiling a text configuration file into an executable Python scripts.


Optional Python Libraries

For running on a cluster using drmaa, i.e. using -b drmaa, you will need to install:


Please refer to kronos online documentation.


email: Jafar Taghiyar <>

Please report issues in our kronos google group.

Change log


  • added a mechanism to update the requirements of the implicit merge via GENERAL section. Note: you can switch off the implicit merge and use an explicit merge if you want to specify a particular requirement for only that merge task.

  • previously, multiple identical implicit merge tasks could exist in a workflow. In the new version, they are combined into a single merge task that happens only once.

  • added a switch called merge that defaults to True in the run subsection of each task. If it is set to False, the implicit merging mechanism is switched off for that task and the following warning message is shown when initializing the workflow:

    UserWarning: Implicit merge is off for task <the_task_name>.
    You may have to use an explicit merge task.
  • added support for tags in the interval file, i.e. an optional tag can be added for each chunk in each line of the interval file that will be used as the suffix for the name of the task corresponding to that chunk. The tags should be added to each line using tab as the separation character, e.g.:

    chunk1     tag1
    chunk2     tag2
    chunk4     tag4
  • bug fixes.


  • each task in the configuration file now has its own requirements entry in the run subsection which takes precedence over the requirements listed in the GENERAL section. This enables users to have different versions of the same requirements for different tasks.
  • interval file now takes precedence over the synchronization, i.e. if a task has an interval file, then it will not be synchronized with its predecessors.
  • added support for floating point memory requests.
  • made all the merged files to store in a directory called merge.
  • username and version are automatically added to the config files when using make_config command.
  • added a check to make sure that the input of the implicit merge node is always a list.
  • bug fixes.


  • Kronos now uses multithreading instead of multiprocessing.


  • removed the limitation on the number of simultaneous jobs/pipelines.
  • added --no_prefix back to the input options of run command.
  • minor bug fixes.


First version released!

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for kronos-pipeliner, version 2.3.0
Filename, size File type Python version Upload date Hashes
Filename, size kronos_pipeliner-2.3.0-py2-none-any.whl (41.9 kB) File type Wheel Python version py2 Upload date Hashes View hashes
Filename, size kronos_pipeliner-2.3.0.tar.gz (33.6 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page