1.6.0

[1.6.0] - 07/03/2025

Added

• Processing of YC data. (Y + mtDNA capture (YMCA))
• Processing of IM data. (Immunocapture)
• conf/Autorun.config:
  • Use hard links when publishing results, instead of copying files.
  • Add YC profile for processing YMCA data.
  • Add IM profile for processing Immunocapture data.
• scripts/create_poseidon_release.sh: New script to create large releases of the entire TF processed data in Poseidon format.
• Now compatible with Pandora Site IDs longer than 3 letters.
  • The following scripts can now infer Site_ID of varied lengths from the Ind_ID (pyPandoraHelper):
    • scripts/clear_results.sh
    • scripts/clear_work_dirs.sh
    • scripts/ethical_sample_scrub.sh
    • scripts/run_Eager.sh
    • scripts/update_poseidon_packages.sh
  • The following scripts can now infer Site_ID of varied lengths from the Ind_ID (rPandoraHelper):
    • scripts/prepare_eager_tsv.R
    • scripts/fill_in_janno.R
• Refactor how valid analysis types are determined in shell scripts, to make more easily extendable.
• scripts/prepare_eager_tsv.R:
  • Now uses Main_Individual_ID instead of Full_Individual_ID as the Sample_Name when one is provided.
  • Now excludes sequencing entries with the Exclude flag set to Yes.
• scripts/create_processed_ind_list.sh: Script to create a list of processed individuals across all analysis types, and a count of individuals in each analysis type.

Fixed

• scripts/run_Eager.sh: Java garbage collector now limited to one thread to avoid memory issues and hanging spawner jobs.

Dependencies

• pyPandoraHelper=0.2.1
• rPandoraHelper=0.2.0

Deprecated