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

v24.09.1

• Fix ngi_report deployment

v24.09 monthly release

• Fix Interop path in demultiplex pipeline
• Increase resources for bcl2fastq and seqreports
• Clean up nextflow workdir when site upps
• CheckQC v4.0.5
• Add sis-style-checksum to sequencing-report-service
• MultiQC v1.24.1
• multiqc ngi 0.8.1
• ngi_reports latest
• taca latest

v24.07 monthly release

• Python on NGI env to 3.11
• Sarek to 3.4.2
  • aswcli to 2.15.57
  • vep-108.2
  • snpeff-5.1
  • Add GRCm39 and WBcel235
  • Increase FASTQC mem in config
• RNAseq to 3.8.1
• Updates to Arteria Seq Report
• Validation plugin at 1.1.2 for nfcore demultiplex and sarek
• Nextflow to 24.04.01
• Add nf-prov at 1.2.1
• Add nf-tower at 1.6.3
• Download nextflow plugins
• Update nf-core commands
• Update ngi_pipeline for latest sarek
• Update snpseq metadata service
• Update TACA dependencies
• MultiQC to v1.22.3
  • multiqc_ngi to 0.8.0
• ngi_reports: Fix bug that the lane yield and Q30 values are inconsistent in the html and txt files
• Turn off megaqc for sthlm for now
• Arteria: Install dependency version specified in the requirements
• CheckQC to v4.0.4

v24.04

• updated ngi_reports, taca, taca_ngi_pipeline to latest
• updated CheckQC to v4.0.2
• updated sequencing report service to v1.5.0
• updated nf-core to v2.13.1
• added nf-core/demultiplex to the deployment
• added snpseq-metadata-service

v24.03 monthly release

• MultiQC to 1.21
• multiqc_ngi to 0.7.2
• TACA to latest
• flowcell_parser to latest
• ngi_reports to latest with grus updates
• Add Leptidea sinapis to fastq_screen for Sthlm

v24.02

What's Changed

• Update multiqc to 1.19, TACA to latest(1.0.0) by @aanil in #219
• Dataops 509 arteria delivery fastq readme by @b97pla in #221
• Set log level to INFO for arteria-checksum by @matrulda in #222
• increase the kong timeout by @b97pla in #223
• use arteria-delivery version v3.1.0 instead of commit hash by @b97pla in #224
• Monthly merge to main by @b97pla in #225

Full Changelog: v23.12...v24.02

v23.12 monthly release

Updates in this release

• MultiQC to 1.18
• TACA to latest
• checkqc to v4.0.0
• seqreport service to v1.4.2

v23.11 production release

What's Changed

• MultiQC to 1.17, TACA to latest, Remove dependency for ngi_reports by @aanil in #204
• snpseq-archive-upload v1.1.1 by @b97pla in #205
• Remove ngi visual version by @slohse in #207
• Monthly by @b97pla in #208

Full Changelog: v23.10...v23.11