v26.01 Monthly release

Changes:

• TACA updated to 32b22336a4a5262d89fb60f37de249c5ad86945e
• Folder structure updated in nf-core pipeline delivery README:s
• MultiQC updated to v1.33
• multiqc_ngi updated to 0.9.5
• ngi_pipeline updated to 3697766dfa9d9f5482bfe914638be3b1188daac0
• ngi_reports updated to d3d20d8ebc02af38e2ecc9e805d1695fc89aa159

v25.11 Monthly release

Changes:

• ngi_reports updated to v1.1.2 - bugfix for AVITI lane 0 issue
• TACA updated to v1.6.12 - improved logging
• flowcell_parser updated to remove couchdb requirement
• New script create_rnaseq_samplesheet.py‎ in sthlm standalone_scripts

v25.09 Monthly release

Changes:

• arteria-delivery updated to v3.3.0 and is now run in a py3.13 virtual environment
• funk_004 crontab updated: Absolute paths and sleep 60 added to Supervisord and Kong commands
• Updated multiQC version to 1.31 and added no_ai: true to config to exclude AI buttons
• MultiQC NGI updated to 0.9.4

v25.08 monthly release

• Remove plot rendering of Multiqc in Stockholm
• ngi_reports: Adds support for Aviti project summary reports, Fixes bug of missing order date in report
• Updated charon timeout intervals in ngi_pipeline
• Switched out couchdb with cloudant in TACA
• Switched out couchdb with cloudant in taca_ngi_pipeline, removed GRUS code

v25.06 monthly release

• Bump sequencing-report-service to v1.5.3-rc1 (#336)
• Update TACA version (#338)
• Increase timeout for bcl2fastq process (#339)
• Downgrade container for BISMARK_ALIGN as a workaround for FelixKrueger/Bismark#652 (comment) (#340)
• Add FastQC options key to miarka_ngi_config.yaml.j2 (#341)
• Update CheckQC to v4.1.0 (#342 and #343)

V25.05 monthly release

• Merge Bimonthly into monthly (#332)
  • Import changes from monthly (Update bimonthly to match monthly #283, Import changes from monthly into bimonthly #301)
  • Fork rnaseq (Download nf-core/rnaseq from forked repository #302, Follow nf-core naming for pipeline releases #319)
  • Upgrade Nextflow, rnaseq and sarek (update nf-core/rnaseq to v3.12.0 #254, Update methylseq and nextflow #316, Add temporary fixes to nf-core/tools#3430 #324, Fix pipeline deployment #325, Fix pipeline aliases #327, Hardcode path to igenomes #328, Hardcode --project #329, Turn off parameter validation for sarek #331)
  • Update TACA (Update TACA version and add config file #296)
• Include new delivery readme for Element data. Update taca-ngi-pipeline and ngi_reports (#333)

v25.03 monthly release

• (docs) Clarify instructions for restarting arteria services
• updated TACA, fix for ONT delivery
• Update ngi_report to make ONT reports
• Increase bcl2fastq timeout to 48h

v25.01 monthly release

• Increase timeout limits for arteria-delivery
• Update nf-core/demultiplex to 1.5.4
• Update nextflow to 24.04.2
• Update sequencing-report-service to v1.5.2
• Update delivery README files for Sarek BPA
• Revert cleanup = False for upps
• Bugfix for TACA runfolder deliveries
• Update TACA to handle ONT deliveries
• Update ngi_pipeline to include aviti runs
• Update MultiQC to 1.26

v24.12 monthly release

• MultiQC
  • update repo path
  • update MultiQC to v1.25.2 to fix kaleido issues
  • update multiqc_ngi to 0.9.2 to use cloudant_python_sdk
• Bump TACA to latest
• snpseq_packs v8.0.4 improvements for ngi_uu_workflow:
  • Exclude .nextflow directory while updating checksums after demultiplexing.
  • Skip md5sums module in demultiplex pipeline .
• (Uppsala) send out E-Mail with current disk usage on every Monday

v24.11 monthly release

• arteria_delivery_version: v3.2.2-rc2
• MultiQC to 1.25.1
• multiqc_ngi to 0.8.2
• Updated github repo urls of taca_ngi_pipeline, sthlm standalone_scripts and flowcell_parser
• Use miniforge to create conda envs instead of miniconda
• Remove legacy python2 NGI env