v0.13.0

Introduced a new ingestion module: Galaxy

Updated the following translation / ingestion modules:

• CWL ingest
• Nextflow translate

Major refactoring to integrate fromcwl and fromwdl into the main Janis CLI. Not backward compatible with <= janis v0.12.x

v0.12.1

Added Nextflow Translation Support
Bug fixes

v0.11.9

Fixes #67 - missing services configuration in janis-generated cromwell config files

v0.11.8

Bug fix of filescheme.py in workflowmanager to handle secondary files of conditional outputs

v0.11.7

use sha3

v0.11.6

• Apply pre janis hook if exists
• Auto load singularity of loading command exists

v0.11.5

Updated sbatch job dependency command

0.11.5

Update sbatch job dependency command

Janis Prepare + Input Transformations + Job Files

Lots of important changes to Janis and some minor backwards incompatible changes

• Changes in JanisConfiguration
  • some keys have been renamed, notably in Cromwell (https://janis.readthedocs.io/en/latest/references/configuration.html#cromwell)

Extended templates, better docs and stability

This is another janis-assistant release that ended up with a chunk of changes: v0.7.13...v0.7.14

NB: This change requires janis-core v0.7.8 (pypi)

CLI methods:

• new janis docs to take you to the docs - anywhere ;)
• Revised argument groups for janis run -h

Templates can now be extended through the janis.templates extension. See the new repo: https://github.com/PMCC-BioinformaticsCore/janis-templates for more information on editing existing and creating your own templates.

Stability changes for MariaDB for singularity (MariaDB/mariadb-docker/issues/262)