February 2022

Updates:

• Nextflow 21.04.3-all
• ampliseq 2.0.0
• viralrecon 2.2
• nf-core tools 2.1
• rnaseq 3.3
• python2 -> python3
• RNASeq delivery README added to TACA config
• Click 7.1.2

October 2021

Updates:

• fix a problem with an extra space in upps_taca_sarek_wes_delivery.yml
• new folder structure for Sarek delivery

September 2021

Updates

• Update MultiQC to 1.11
• Fix for cronjob launching kong
• TACA version bump
• Sarek updates
  • --generate_gvcf added as default parameter
  • TACA config and Readme added for WES analysed with Sarek for Upps.

June 2021

• remove applyrecalibration
• remove bam2fastq
• Cleanup unused links ngi pipeline
• archive-upload-ws to v1.0.4
• sarek to 2.7

May 2021

Updates

• methylseq (1.6->1.6.1)
• ampliseq (1.1.2->1.2.0)
• atacseq (1.1.0->1.2.1)
• multiqc (1.10->v1.10.1)
• snpseq-archive-upload (1.0.2 ->1.0.3)
• taca-ngi-pipeline
  • Updates to Sthlm delivery Readmes.

April 2021

This monthly release contains the following updates:

• nfcore/methylseq: Version bump to v1.6
• nfcore/nanoseq: New addition at v1.1.0
• TACA: Updates to NextSeq2000 flow and additional 10x index types and masks
• Flowcell parser: Updates to NextSeq 2000 flow
• multiqc: Remove the temporary matplotlib fix at v3.2.2 (fixed in multiqc v1.10).
• ngi_reports: Update to account for changed library construction values.

March 2021

This monthly release contains the following updates

Additions

• Add rnafusion v1.2.0

Updates and fixes

• Update rnaseq to v3.0
• Multiqc: Updated to v1.10
• Update nexflow version to v20.11.0-edge
• Update ansible version to 2.9 and related playbook updates
• Arteria updates
• taca-ngi-pipeline: Add new RNASeq and Sarek delivery readmes for Sthlm.
• TACA: Various updates to support NextSeq2000.
• ngi-pipeline : pinned inflect for py2.7.
• Flowcell parser: Fix data format for NextSeq2000.
• ngi_reports: Support for NextSeq2000 and updates to text from SWEDAC regarding deviations.

Feb 2021

This monthly release contains the following updates:

• ngi_pipeline
  • ported to py3
  • QC jobs are given more time
  • remove the not_as_million and update based on number of reads
• TACA
  • New delivery README:s for sthlm
• Arteria delivery
  • Patch update to solve an install issue

First release on new monthly schedule

General Changes

We are now switching to a new monthly release schedule, where updates are first merged to and deployed to stage form the Monthly branch. The updates are pushed to master only for production deployments. The schedule may have some releases which club two months for tools which require extensive testing and validation.

Tool Updates

• ngi-reports - code refactored ( no change in functionality ).

• TACA - removal of unused code

• taca-ngi-pipeline - bugfixes in xml generation.

• ngi-pipeline - removal of unused code

• multiqc - fix matplotlib to version 3.2.2 to suppress warnings.

New deployment strategy for containers and ngi_pipeline support for sarek v2.6.1

General changes

Containers are now added to a directory outside the versioned deployment directories: /lupus/ngi/containers/. The reason for this is to avoid downloading all containers to every environment version. Using this approach makes deployment faster and make the deployment take up less space.
​
The following software are no longer deployed:

• arteria-siswrap
• neutronstar
  ​

Changes per role

​

• MultiQC

  • Updated to v1.9
  • MegaQC details added to Uppsala's config
    ​

• nf-core

  • Added nfcore/viralrecon
    ​

• sarek

  • Updated to v.2.6.1
  • The apply_recalibration script is now adapted for sarek and managed in this role (previously in ngi_pipeline repo)

• ngi_pipeline

  • Support for Sarek v2.6.1 added
  • Updated Charon timeout limit
    ​

• anaconda

  • New python 3.8 environment added (called NGI_py3)
    ​

• ngi_reports

  • Updated version that runs on py3 (py2 no longer supported) and dependency to pandoc has been dropped
  • No longer used by Uppsala
    ​

• nextflow

  • Uppsala's nextflow config do no longer specify to run MultiQC processes locally
    ​

• TACA

  • Updated version
  • Configs added for staging sarek data