New arteria-delivery version (v2.1.0)

arteria-delivery has been updated and is now able to show staged runfolders to operators

New release of NGI-RNAseq and MultiQC

• NGI-RNAseq have new release v1.3.1 which includes refactoring of process RSeQC to make pipeline faster. It also have other changes which can be seen here.

• MultiQC have new release v1.3 with new modules. Complete list can be found here

• CAW - Cancer Analysis Workflow is now included in the playbook. This is still going to be for testing purpose

• nextflow - Recipe hardcoded for version 0.25 as the latest version needed JAVA 8+

MultiQC dependancy fix and ngi_reports updates

• MultiQC: Dependancies of MultiQC were build on specific version of their dependancy. Installs specific version of requirement.

• ngi_reports: Adapt the report template for GRUS delivery and also couple of features that might be useful for MiSeq runs

• ansible: Added ssh options for performance improvement

arteria-delivery webservice version 2.0.0

Main change is that we're now rolling out latest stable version of arteria-delivery webservice (2.0.0).

Release also removes some unwanted aliases for ngi-methylseq.

Updated Pipelines and tools

• NouGAT and NGI-MethylSeq updated. Among other things use Singularity images for improved performance and stability.
• Various arteria-delivery bugfixes and management updates
• Tarzan has now an easier time relaunching Kong services
• Nextflow upgraded to latest version (0.25)

Delivery systems hotfixes

• Arteria-delivery upgrades
• Mover orderportal support
• Version updates of ngi_pipeline, taca-ngi-pipeline, ngi-rnaseq and ngi_reports
• Readme updates
• NGI_Pipeline symlinked folders fix
• Statusdb configuration is now part of the TACA playbook

New delivery systems

• Arteria-delivery now launches specific version of mover + fixed issue with how supervisord launches the web service
• UGC has got a new version of their delivery script installed, which also calls a specific version of mover + sets whether data is sensitive or not
• TACA deliveries through Mover is fully functional by merit of updating TACA, NGI-Pipeline and taca-ngi-pipeline to version 0.6.13.0, 0.1.10 and 0.6.0 respectively
• NGI-Pipeline now has integrated genotype concordance, an attached ACKNOWLEDGEMENTS file for referencing and a travis self test
• TACA has been updated to better handle NoIndex sequencing runs.
• MultiQC along with it's NGI plug-in, have been updated to version 1.0 and 0.4 respectively to resolve some known bugs
• NGI-RNAseq have been updated to version 1.1 and now has related TACA delivery script
• Stockholm specific TACA deliveries are now done to Projectname-PID as opposed to the prior PID

Hotfixes for v.1.7

Version v1.7 was a major release introducing several new software. This release (v.1.7.1) applies fixes for the following solutions:

• Arteria-delivery, fixes in regards to mover and supervisord
• NGI-RNASEQ, exchanged temporary files directories
• Multiqc, fixes for report delivery issues for staging environment

Major releases and updates of many softwares

• Arteria delivery v1.0.0 release
• NGI-rnaseq release version
• TACA cleanup function was increased in efficiency and now handles undetermined reads better
• Genotype concordance script for NGI_Pipeline is now deployed
• NouGAT now has KmerGenie available as an option for k-mer plot generation
• Nextflow dependency had a few bug fixes
• NGI_Pipeline was updated for better interaction with fastq_screen
• MultiQC NGI plugin now produced improved layout
• NGI_Reports now support project name report generation
• TACA now (also) prints log info to standard output

Urgent piper version update

• Piper module call updated to version 1.5.1
• Irma-provisioning readme updated
• Configuration for NGI-Pipeline (gt_concordance) updated
• Configuration for TACA (taca cleanup) updated