v0.13.1

Update all janis components (release notes are available in each repository):

janis-unix 0.12.0
janis-pipelines 0.13.0
janis-bioinformatics 0.12.2
janis-core 0.13.1
janis-assistant v0.13.0
janis-templates 0.12.0

Bug fixes:

WDL output translations from the CLI is now working again
Updated nextflow translation from Janis to fix edge cases
Updated galaxy ingest

v0.13.0

Update all janis components (release notes are available in each repository):

janis-unix 0.12.0
janis-pipelines 0.12.0
janis-bioinformatics 0.12.2
janis-core 0.13.0
janis-assistant v0.13.0
janis-templates 0.12.0

v0.12.0

Update all janis components (release notes are available in each repository):

janis-unix 0.12.0
janis-pipelines 0.12.0
janis-bioinformatics 0.12.1
janis-core 0.12.1
janis-assistant v0.12.1
janis-templates 0.12.0

v0.11.6

Update all janis components (release notes are available in each repository):

• janis-unix 0.11.2
• janis-pipelines 0.11.5
• janis-bioinformatics 0.11.3
• janis-core 0.11.5
• janis-assistant v0.11.9
• janis-templates 0.12.0

v0.11.4

use sha3

v0.11.3

Merge pull request #48 from PMCC-BioinformaticsCore/upgrade-v0.11.3

upgrade to v0.11.3

v0.11.2

• Update Spartan template to run in the background by default .
• Auto load required Spartan modules.
• If Slurm template has instructions to load singularity, it will automatically load it.

v0.11.1

Added janisdk run-test command line tool

Stability improvements + deprecating cwlgen

Multitude of little feature improvements, new tools and stability fixes.

• Removing cwlgen: Notably in this release I've removed python-cwlgen in favour of cwlutils. You can read more, and find the linked issues in PMCC-BioinformaticsCore/janis-core#21.
• Added cwl-format
• Akka changes to Cromwell
• SQLite refactor for stability in janis-assistant

General improvements + new tools

This general release of Janis combines a number of improvements from the individual components. I'd like to highlight the new structure of tools (better quickstart guides), and a set of updated guides and tutorials.

General improvments:

• New guides and documentation
• Replace pkg_resources with importlib_metadata to improve import times

Janis Core:

• Support for Python 3.8
• Add metadata to Workflow and CommandToolBuilder
• Improve error messages
• Allow no containers with flag allow_empty_container=True or --allow-empty-container
• Refactor "registry" to be called "Toolbox"
• New ability to document types of inputs, see example

CWL:

• Fixes CWL localisation for Arrays
• Adds SHEBANG to CWL
• Add "is_packed" during API translation for a packed workflow.

Janis Assistant

Changes in behaviour:

• Configuration file is only loaded on run and translate, both of these methods allow override with -c.
• When loading a python file (janis translate file.py ...), Janis now chooses the workflow if 1 is available, else still require the --name param.

New:

• Improve recipe directory + path from environment variable detection.
• Check all input files are present before running (skip with --skip-file-check)
• Disable adding tasks to central DB with --no-store
• Add "batchrun" functionality to run the same pipeline easily across multiple samples.
• Copy workflow logs, even when workflow fails
• Cromwell memory override options
• Input template generation now has --user, --static, --recipes

Bugs:

• Fixed template initialisation bugs
• Input paths would not be fully qualified if in an array
• Starting janis with verbose method would cause workflow start to fail.
• Reduce likelihood of sqlite errors when watching or viewing a workflow's metadata.

Janis Bioinformatics

Data types:

• New Cram filetype
• Fasta references:
  • Fasta reference fixes
  • Fixed inheritance from Fasta subtypes
  • New FastaBwa type: #23
• New Compressed FASTA types #25.

New tools:

• BamSorMaDup
• Gatk4MergeBamAlignment
• Gatk4FastqToSam
• Scramble (IO)
• Indexing tools:
  • Index Fasta (pipeline)
  • Bwa Index
  • Samtools Index
  • Gatk4CreateSequenceDictionary

Contributions

We'd like to extend thanks to contributors for this release @matthdsm, @rlupat, @SebastianHollizeck and more.

We're very appreciative of those using or testing Janis. We'd like to hear from you by raising issues or jumping on the Gitter.