Code

V12 pathology (13/N)#335

Code

Merged

jharenza merged 138 commits intov12-lggd3b-center/OpenPedCan-analysis:v12-lggfrom v12-pathd3b-center/OpenPedCan-analysis:v12-pathCopy head branch name to clipboardApr 29, 2023

+106,972-73,122

Commits

Commits on Mar 3, 2023

• update compile v12

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• Merge branch 'v12-epn' into v12-path

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• Merge remote-tracking branch 'origin/v12-lgg' into v12-path

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• run path subtyping

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Commits on Mar 9, 2023

• Merge branch 'v12-lgg' into v12-path

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• update path

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• Merge branch 'v12-epn' into v12-path

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• update files

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• Merge branch 'v12-lgg' into v12-path

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• initial run of integrate

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• update efo mondo file, few cancer groups

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Commits on Mar 20, 2023

• Merge remote-tracking branch 'origin/v12-lgg' into v12-path

  

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• rerun with updated v12 data release

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• rerun with updated v12 release

  

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Commits on Mar 22, 2023

• rerun with v12 ef-mondo-ncit map

  

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• v12 independent sample lists

  

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Commits on Apr 13, 2023

• merge v12-lgg

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• re-run the module

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• merge v12-path

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• re-run the module

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• merge v12-integrate

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• re-run the module

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• update Other tumors (all histiocytic JXG)

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• Merge remote-tracking branch 'origin/v12-lgg' into v12-path

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• rerun

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• Merge branch 'v12-path' into v12-integrate

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• rerun module

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Commits on Apr 14, 2023

• Merge branch 'v12-atrt' into v12-path

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• rerun with hgg changes

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• Merge branch 'v12-path' into v12-integrate

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• rerun with hgg changes

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• Merge branch 'v12-atrt' into v12-path

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• rerun

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• Merge branch 'v12-path' into v12-integrate

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• add mol subtype methyl in compiled file

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• Merge branch 'v12-path' into v12-integrate

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Commits on Apr 17, 2023

• merge v12-lgg

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• re-run the module

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• merge v12-path

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• re-run the module

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• merge v12-integrate

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• re-run the module

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Commits on Apr 18, 2023

• Merge remote-tracking branch 'origin/v12-lgg' into v12-path

  

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• PR stacking reruns

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• PR stacking reruns

  

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• Merge remote-tracking branch 'origin/v12-lgg' into v12-path

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• set unmatched low confidence methyl to NA

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• set unmatched low confidence methyl to NA

  

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• resolve methyl duplicates

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• resolve methyl duplicates

  

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• add GNT NOS to path dx for gnts

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Commits on Apr 19, 2023

• Merge branch 'v12-lgg' into v12-path

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• remove NOS from tumors that are have subtypes!

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• Merge branch 'v12-lgg' into v12-path

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• rerun

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• Merge branch 'v12-path' into v12-integrate

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• rerun

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• remove duplicates

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• Merge branch 'v12-path' into v12-integrate

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  da3dfef

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• remove discrepancies

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• Merge remote-tracking branch 'origin/v12-lgg' into v12-path

  

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• rerun

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• rerun

  

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• Merge remote-tracking branch 'origin/v12-emb' into v12-path

  

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• rerun

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• rerun

  

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Commits on Apr 20, 2023

• Merge branch 'v12-lgg' into v12-path

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• rerun without DGD samples

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• rerun without DGD samples

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• Merge branch 'v12-path' into v12-integrate

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• rerun without DGD samples

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• Merge branch 'v12-lgg' into v12-path

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• rerun with updated LGG

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• Merge branch 'v12-path' into v12-integrate

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• rerun with LGG update

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Commits on Apr 21, 2023

• Merge branch 'v12-lgg' into v12-path

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  7d5b198

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• rerun

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• Merge branch 'v12-path' into v12-integrate

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  dcd606d

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• rerun

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• update cancer group

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• Merge remote-tracking branch 'origin/v12-emb' into v12-path

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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Commits on Apr 25, 2023

• Merge remote-tracking branch 'origin/v12-lgg' into v12-path

  

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• rerun with updated pre-release data

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• rerun with updated pre-release data

  

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• Merge remote-tracking branch 'origin/v12-integrate' into v12-independent-samples

  

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• rerun with updated final histologies

  

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• update to compile new epn subtyping file

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• rerun with new compiled epn subtyping file

  

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• Merge branch 'v12-epn' into v12-path

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• rerun with epn update

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• Merge branch 'v12-path' into v12-integrate

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• rerun hist with epn update

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• Merge branch 'v12-hgg' into v12-path

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• rerun with hgg updates for path dx subset

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• Merge branch 'v12-path' into v12-integrate

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• rerun with latest hgg

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• Merge branch 'v12-hgg' into v12-path

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• rerun with hgg update

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• Merge branch 'v12-path' into v12-integrate

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• update HGG cancer groups

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• Merge branch 'v12-emb' into v12-path

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• Merge branch 'v12-emb' into v12-path

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• rerun with updated emb

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• rerun

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• Merge branch 'v12-path' into v12-integrate

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  1c76d6e

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• rerun with updated emb

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• Merge branch 'v12-emb' into v12-path

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• rerun with emb

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• Merge branch 'v12-path' into v12-integrate

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  b2c2cb4

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• rerun

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Commits on Apr 26, 2023

• Merge remote-tracking branch 'origin/v12-lgg' into v12-path

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• update samples 7316-6047

  

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• update samples 7316-6047

  

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• update samples 7316-6047

  

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• Merge remote-tracking branch 'origin/v12-path' into v12-integrate

  

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• update samples 7316-6047

  

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• Merge remote-tracking branch 'origin/v12-integrate' into v12-independent-samples

  

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• rerun with updates final histologies

  

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• v12 CI subset files

  

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Commits on Apr 27, 2023

• update dockerfile to use debian stretch archive

  

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• update molecular-subtyping-MB to run with CI subsets

  

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Commits on Apr 28, 2023

• update subtyping module to run with CI subsets

  

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• update tp53 to run with CI subsets

  

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• Merge pull request #355 from PediatricOpenTargets/v12-subset-files

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• exclude immuned deconvo from GA checks

  

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Commits on Apr 29, 2023

• Merge pull request #344 from PediatricOpenTargets/v12-independent-samples

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• Merge pull request #336 from PediatricOpenTargets/v12-integrate

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