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3.1.7

  • updated CWL metadata schema IRI

3.1.6

3.1.5

  • Update cgpCaVEManWrapper to allow parallel flagging in cgpwgs layer

3.1.4

3.1.3

  • Update base image to dockstore-cgpmap:3.1.4

3.1.2

  • Add security updates to image build
  • Update base image to dockstore-cgpmap:3.1.2
  • Update caveman related versions to pick up hotfix to protect against corrupt index files
    • CaVEMan 1.13.15
    • cgpCaVEManWrapper 1.13.13 (just to keep in sync)

3.1.1

  • Update to dockstore-cgpmap:3.1.1 for base image
  • Bump vcftools to 0.1.16 - security
  • Allow jobs to resume when process scripts exist, long since proven double run doesn't occur
  • Ensure that ENA server is never used for CRAM processing
  • New versio of cgpCaVEManPostProcessing to solve memory problems in flagging when using BED files, also bumps vcftools

3.1.0

  • Update to dockstore-cgpmap:3.1.0 for base image
  • Update dependencies to support fragment based read counts (and other fixes):
    • cancerit/cgpPindel - v3.1.2
    • cancerit/cgpCaVEManPostProcessing - 1.8.6
    • cancerit/cgpCaVEManWrapper - 1.13.12
    • cancerit/CaVEMan - 1.13.14
    • cancerit/VAGrENT - v3.3.3
  • Drop expected tree, will be revising how verification of container is achieved.

3.0.3

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

3.0.2

Bumps versions of dependencies to bring in

  • Official release of Bio-DB_HTS
  • Alternate use of tabix query to allow contigs with names containing colon.

3.0.1

Updates to relating to:

  • PCAP-core
    • Add threaded processing to bam_stats to reduce overall runtime.
  • CaVEMan
    • Fix bug in error handling and exit codes.

3.0.0

  • See dockstore-cgpmap v3.0.0 (primarily adds mismatchQc)
  • 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.

2.1.0

  • Fixes various sort order issues in CaVEMan, cgpPindel and VAGrENT affecting comparison of results from same inputs.

2.0.7

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

2.0.6

  • Update base image to dockstore-cgpmap:2.0.3 (new PCAP-core for load management)
  • Bump cgpCaVEManWrapper to gain access to split size tuning (not used here)

2.0.5

Very minor modifications to reduce potential issues from CPU oversubscription.

2.0.4

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

2.0.3

  • Fixed cgpPindel

2.0.2

  • Update cgpPindel to reduce usage of Capture::Tiny apparent cause of some failures.

2.0.1

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

2.0.0

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

1.0.4

  • Updates base image to add load management facilities via ENV variables.

1.0.3

  • Add params file to output bindings

1.0.2

  • Fix up output files slightly
  • Update base image for dependency (PCAP-core etc)

1.0.1

  • Fixes handling of species/assembly
  • Update base image (PCAP-core etc)

1.0.0

Initial release of flow