v8.2.0

Note

• Run vip.sh instead of vip
• Please perform a clean install instead of reusing previously downloaded images and resources

What's Changed

• Installer overhaul by @dennishendriksen in #675
  • install with oneliner: curl -sSL https://download.molgeniscloud.org/downloads/vip/install.sh | bash
  • faster install
    • verify checksums during download
    • only verify checksums for newly downloaded resources
    • reuse previously downloaded resources
  • check requirements
    • bash & bash version
    • java & java version
    • apptainer
    • free disk space
  • use environment variables
    • instead of command-line options
    • instead of symlinks
    • to allow better integration with EasyBuild
  • reduce diskspace requirements by 30GB
  • rerunning install command will install latest vip version
  • report when slurm if available and mention that vip will use it automatically
  • other small stuff
    • better logging
    • better cleanup on errors
    • check if vip version exists and is supported by installer
    • remove dependency on git
    • resolve "chmod: changing permissions of ‘nextflow-24.10.3-dist’: Operation not permitted" warning
    • change: does not download GRCh37 reference genome
    • change: rename /install.sh to /install_data.sh, move /utils/install.sh to /install.sh
    • change: versions installed with '/' are installed in corresponding folder with '_' (e.g. feat/report will be installed in feat_report)
    • change: do not check for latest nextflow version, resulting in supression of warning
    • change: run vip.sh instead of vip
• Short variant phasing using Whatshap by @bartcharbon in #674
• Update inheritance matcher v3.3.5 to v3.3.6 by @bartcharbon in #674
• Add default WES and WGS .bed files for coverage calculation by @bartcharbon in #672
• Update report template from v7.1.0 to v7.1.1 by @bartcharbon in #673
• Fix Apptainer bind warnings by @dennishendriksen in #676
• Fix update capice_model v5.1.2-v3 to v5.1.2-v4 by @dennishendriksen in #675
• Fix update vkgl 20240701 to 20241001 by @dennishendriksen in #675
• Fix install AnnotSV exomiser resources in correct directory by @dennishendriksen in #675

Full Changelog: v8.1.1...v8.2.0