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2.0.0 - support for both singularity and GRCh38

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@keiranmraine keiranmraine released this 06 Jul 12:42
· 50 commits to develop since this release
2.0.0
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keiranmraine Keiran Raine
GPG key ID: 2CA6274992A32EE2
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2.0.0

Major work to enable support for both singularity and GRCh38. Note that there may be an additional release to handle an efficiency issue in cgpPindel under GRCh38. Reference bundles for GRCh38 are not yet public.

  • 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
  • First official support for Singularity (extra variables and documentation)
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