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2.1.1

  • updated CWL files metadata schema IRI
  • updated R's GPG key

2.1.0

  • Update base image to dockstore-cgpwxs:3.1.6 (from 3.0.3)
    • Includes, memory footprint reduction for Caveman flagging
    • Significant speedup in inde input generation
    • Parallel flagging for SNV
    • Fragment based SNV/Indel calling
  • Upgrade allele counter and brass
  • Reduce number of layers in final image.
  • Remove some legacy env vars from wrappers
  • Battenberg removed
    • Was only included to do base allele counts not complete analysis
    • Underlying data files are not supported for new builds or other species
    • Contact original authors for ongoing support
  • Wrapper script didn't explicitly specify sex SNP loci file (ASCAT)
    • no impact for GRCh37 other species/build would have used wrong sex chromosome SNPs
  • CaVEMan step wasn't being passed normal contamination value, scientific impact:
    • previously caveman.pl default of 0.1 was applied
    • this will now honor the value from ASCAT (1-$rho)

2.0.2

  • Correct skipqc flag

2.0.1

  • Add param to skip QC related steps that rely on heterozygous data.

Merge back-port into mainline:

  • 1.1.4
    • Provide parameter to allow user to lower max pindel threads for analysis proving to have huge memory spikes
    • Add -force to ascat.pl execution, seems to have been lost along the way

2.0.0

  • Full support for BAM+CSI and CRAM+CRAI as inputs
  • Reorganisation to allow access of other tools or necessary bindings
  • See dockstore-cgpmap 3.0.0 - 3.0.4 (primarily adds mismatchQc and threads to some tools)
  • See dockstore-cgpwxs 3.0.0 - 3.0.3 (fragment based analysis)
    • You will need to update the reference pack to include the new flagging rules, see example json files
  • Using build stages to shrink images.
  • remove legacy PRE/POST-EXEC from cgpbox days
  • resolves #17, #18, #19, #20, #21, #24

1.1.2

  • BRASS, random seed fixed to make noisy data have a reproducible result:

1.1.1

  • Stable results between replicate runs:
    • see v6.0.3
    • took multiple executions of 29 datasets to find this edge-case.

1.1.0

BRASS updates

  • Significantly reduces the run time of brass_group phase
    • see v6.0.0
    • Requires new version of the CNV_SV reference archive
  • Ensure stable result between replicate runs:

Other dependency updates

Workflow updates:

  • Reorganisation of some processes to reduce run-time:
    • Changes to alleleCount have vastly improved I/O pattern and reduced runtime for ascat and IMPUTE-allele counts (pre-Battenberg).
    • Reduced number of split files for IMPUTE-allele counts as reduced run time negates need for large spread
    • Reduced alleleCount runtim allowed reorganisation of processes reducing runtime on example data from 23h to 19.5h (28cpu).
  • Added cavereads to example json specifying a higher value than default to reduce jobs required.

1.0.8

  • Update Brass to v5.4.1
    • Provide additional reference file rather than attempt to decode species/build due to the may ways a species can be defined.

1.0.7

  • Update BRASS to v5.4.0
    • Specifically fixes a vector merge bug which produces warnings (but no apparent change to results).

1.0.6

  • Fixes #13 - Parsing of sample name from BAM headers fails is sample at end of line
  • Update dockstore-cgpwxs to 2.0.7 - Fixes bug in pindel core.

1.0.5

  • Improved handling of CPU oversubscription via PCAP-core update in base image
  • Update cgpCaVEManWrapper to expose extra options (specifically split size)

1.0.4

Fix an error in param capture test

1.0.3

  • Export the PCAP_THREADED_* variables
  • Fixed #8, #9, #10
  • Updated base image to pull in fix required for PCAP_THREADED_LOADBACKOFF

1.0.2

  • Update BRASS to handle data that is very quiet
  • Fix up the wrapper timings file so it is captured properly
  • Upgraded base image to dockstore-cgpwxs:2.0.4
  • Remove ability to build *.bas files as not possible to have optional secondary files and we state expectation of dockstore-cgpmap as data source.
  • Moved some processing around to reduce cpu wastage.

1.0.1

  • Update dependencies to reduce reliance on Capture::Tiny, apparent cause of some issues

1.0.0

  • Test data in examples/analysis_config.local.json moved to a non-expiring location.
  • See dockstore-cgpwxs:2.0.0
  • Significant shrinking of image.
  • Re-org of exec order to reduce overall runtime.