3.1.6 - Indel speedup

Update to cgpPindel v3.2.0 for significant speedup in indel input generation step.

3.1.1 - Large decrease in memory footprint

Memory issues with GRCh38 resolved.

Reference files for Human GRCh38 can be found here:

ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/GRCh38_hla_decoy_ebv/

3.0.3 - GRCh38 support work

Bumps dockstore-cgpmap to include new version of dockstore-cgpbigwig for GRCh38 support on generation of bigwig files.

3.0.0

• See dockstore-cgpmap v3.0.0 (primarily adds mismatchQc)
  • actually uses v3.0.1 as base to allow use of csi indexes.
• CaVEMan and cgpPindel updated to use fragment based counting.
  • You will need to update the reference pack to include the new flagging rules, see example json files
• VAGrENT update to v3.3.0, only affects generation of annotation cache not use of existing ones.
• Using build stages to shrink images.
• remove legacy PRE/POST-EXEC from cgpbox days, use dockstore if you want file provisioning.
• Adds minimised expected results to repository so tagged history is available.

2.1.1 - Additional data stability

Physical result unchanged, however ordering of VAGrENT output is now stable.
CaVEMan core has reduced I/O with minuscule cpu overhead.

2.1.0 - fixes for reproducible results

Update caveman, pindel and vagrent to improve reproducibility.

2.0.7 - Update cgpPindel

Bumps cgpPindel to v2.2.3 to fix bug in DI event collation.

Large reduction in temp space and I/O

Large reduction in temp space and I/O for cgpPindel. See cgpPindel-v2.2.0

2.0.1 - update test data location

• Test data in examples/analysis_config.local.json moved to a non-expiring location.

Rework of build process and bug fix

2.0.0

• See dockstore-cgp:2.0.0
• Streamlined install process to reduce build time and size of image.
• Fix to SNV flagging - was not being applied previously.

Please re-download the SNV_INDEL_ref_GRCh37d5.tar.gz file if you have staged this to your local systems.