imgag/megSAP: 2025_10

What's new

• General changes
  • Updated databases and several tools
    • Note that way more transcripts are contained in Ensembl 115. See https://www.ensembl.info/2025/02/14/cool-stuff-ensembl-vep-can-do-reduce-the-number-of-human-transcripts-you-need-to-consider-without-missing-results/ and https://www.ensembl.info/2025/09/02/ensembl-115-has-been-released/.
  • added support for singularity in addition to apptainer
  • updated OS in tool containers to Ubuntu 24.04
  • Illumina DRAGEN
    • simpifiled file handling: renaming files is not longer necessary. Just copy the DRAGEN output into the dragen sub-folder of a processed sample folder.
    • added multi-version installation support by specifying the DRAGEN version in the megSAP settings. Note: only DRAGEN 4.3 is supported right now.
    • removed settings parameter 'use_dragen_sv_calling': Using DRAGEN SV files when they are available because they are way better than Manta (see performance page).
    • added support for ORA as input for DRAGEN
  • ensure consistent fallback to data_folder when local_data copy is missing/incomplete
• germline WES/WGS:
  • DeepVariant is now the default caller for small variants (was freebayes before)
• germline lrGS:
  • added Clair3 GPU support
  • updated Straglr to version 1.5.4
  • improved PacBio support
• germline RNA:
  • updated arriba to version 2.5.1
• somatic tumor-only:
  • renamed the pipeline script to somatic_tumor_only.php
  • improved sensitivity for low AF variants and runtime
• somatic tumor-normal:
  • renamed the pipeline script to somatic_tumor_normal.php
  • added support for WGS

Full Changelog: https://github.com/imgag/megSAP/compare/2025_03...2025_10