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Feature/extract align#126

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buehlere wants to merge 125 commits intodevelopmskcc-omics-workflows/modules-fork:developfrom feature/extract_alignmskcc-omics-workflows/modules-fork:feature/extract_alignCopy head branch name to clipboard

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Commits on Apr 13, 2023

• adding mskcc modules

  

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• adding test yaml for mskccprepnucleo

  

  EricWilliam Buehler

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Commits on Apr 20, 2023

• name change

  

  EricWilliam Buehler

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• removing redundant channel

  

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Commits on Apr 27, 2023

• re-doing first access subworkflow

  

  EricWilliam Buehler

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Commits on May 2, 2023

• clean up old workflow, after re-name

  

  EricWilliam Buehler

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Commits on May 9, 2023

• try fork syncing

  

  EricWilliam Buehler

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• Merge branch 'develop' into feature/extractumi

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• experimenting with auto sync

  

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• Merge branch 'feature/extractumi' of https://github.com/mskcc-omics-workflows/modules into feature/extractumi

  

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• testing gitactions

  

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• gitactions test

  

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• Merge pull request #4 from nf-core/master

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• gitactions experiment

  

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• Merge branch 'feature/extractumi' of https://github.com/mskcc-omics-workflows/modules into feature/extractumi

  

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  fde2b5d

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• trying to fix gitactions

  

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• Create sync-fork.yml

  

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• Update sync-fork.yml

  

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• Update sync-fork.yml

  

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• Update sync-fork.yml

  

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• Merge branch 'master' of https://github.com/mskcc-omics-workflows/modules

  

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• Update sync-fork.yml

  

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• Update sync-fork.yml

  

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• Update sync-fork.yml

  

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• Update sync-fork.yml

  

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• Merge branch 'master' into feature/extractumi

  

  buehlere

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• remove output folders

  

  buehlere

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• adding base template

  

  EricWilliam Buehler

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Commits on May 10, 2023

• Update sync-fork.yml

  

  buehlere

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• Revert "Update sync-fork.yml"

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• Create sync-action.yml

  

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• Merge pull request #10 from nf-core/master

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Commits on May 11, 2023

• Merge branch 'master' into feature/alignment

  

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Commits on May 12, 2023

• Merge pull request #11 from nf-core/master

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Commits on May 13, 2023

• Merge pull request #12 from nf-core/master

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Commits on May 15, 2023

• Merge pull request #13 from nf-core/master

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Commits on May 16, 2023

• Merge pull request #14 from nf-core/master

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Commits on May 17, 2023

• Merge pull request #15 from nf-core/master

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• remove this for separate PR

  

  buehlere

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• Merge branch 'master' into feature/extractumi

  

  buehlere

  committed
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• working alignment example

  

  EricWilliam Buehler

  committed
  05e1212

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• clean up for extractumi

  

  EricWilliam Buehler

  committed
  eaef95a

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• Merge branch 'master' into develop

  

  buehlere

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• Update sync-action.yml

  

  buehlere

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• Delete sync-fork.yml

  

  buehlere

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  ab7ba98

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• Merge pull request #16 from nf-core/master

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• Merge branch 'develop' into feature/extractumi

  

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• Update sync-action.yml

  

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• Update sync-action.yml

  

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• Revert "Merge pull request #16 from nf-core/master"

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Commits on May 18, 2023

• Merge pull request #17 from nf-core/master

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• Update sync-action.yml

  

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• Merge pull request #20 from nf-core/master

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• Merge branch 'develop' into feature/extractumi

  

  buehlere

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• cleanup

  

  EricWilliam Buehler

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• Merge branch 'develop' into feature/alignment

  

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Commits on May 22, 2023

• Merge pull request #23 from nf-core/master

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Commits on May 23, 2023

• Merge pull request #25 from nf-core/master

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Commits on May 24, 2023

• Merge pull request #27 from nf-core/master

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Commits on May 25, 2023

• Merge pull request #29 from nf-core/master

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• Trigger github actions when PR is made against develop

  anoronh4

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• split github workflows into different files for running on develop PRs

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Commits on May 26, 2023

• Merge pull request #32 from nf-core/master

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• Disable sentieon testing in CI pytests for PRs against develop

  anoronh4

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• changed names of all github action workflows that trigger in PRs against develop

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Commits on May 27, 2023

• Merge pull request #34 from nf-core/master

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Commits on May 30, 2023

• Merge pull request #36 from nf-core/master

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Commits on May 31, 2023

• Merge pull request #38 from nf-core/master

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Commits on Jun 1, 2023

• Merge pull request #40 from nf-core/master

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Commits on Jun 2, 2023

• Merge pull request #42 from nf-core/master

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Commits on Jun 3, 2023

• Merge pull request #44 from nf-core/master

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Commits on Jun 5, 2023

• Merge pull request #46 from nf-core/master

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Commits on Jun 6, 2023

• Merge pull request #48 from nf-core/master

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Commits on Jun 8, 2023

• Merge pull request #50 from nf-core/master

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• Merge pull request #30 from mskcc-omics-workflows/enhancement/run_workflows_develop

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• Merge branch 'develop' into feature/extractumi

  

  buehlere

  committed
  b82a132

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• prettier formatting

  

  buehlere

  committed
  e32f380

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• fix formatting for linters

  

  buehlere

  committed
  c588273

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• removing tools-test-dataset

  

  buehlere

  committed
  601c863

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• re-doing md5 sum

  

  EricWilliam Buehler

  committed
  a3ae978

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• Update test.yml

  

  buehlere

  committed
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• redoing md5sums

  

  EricWilliam Buehler

  committed
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Commits on Jun 9, 2023

• Merge pull request #52 from nf-core/master

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• Update main.nf

  

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Commits on Jun 10, 2023

• Merge pull request #54 from nf-core/master

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Commits on Jun 13, 2023

• Merge pull request #56 from nf-core/master

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Commits on Jun 22, 2023

• Merge pull request #58 from nf-core/master

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• Merge branch 'develop' into feature/alignment

  

  buehlere

  committed
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Commits on Jun 26, 2023

• adding bwa2 init

  

  EricWilliam Buehler

  committed
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Commits on Jun 27, 2023

• updating test

  

  EricWilliam Buehler

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• updating how data is pulled for test

  

  EricWilliam Buehler

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Commits on Jun 28, 2023

• updating alignment, first version I'm expecting to work

  

  EricWilliam Buehler

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• remove dangling features

  

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• Delete .gitmodules

  

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Commits on Jul 6, 2023

• fix formatting

  

  buehlere

  committed
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• fixing test

  

  EricWilliam Buehler

  committed
  772cb59

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• Merge branch 'feature/alignment' of https://github.com/mskcc-omics-workflows/modules into feature/alignment

  

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Commits on Jul 18, 2023

• fixing indexing

  

  EricWilliam Buehler

  committed
  2b004a9

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• update testing

  

  buehlere

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  cff132b

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• Update main.nf

  

  buehlere

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Commits on Aug 8, 2023

• Merge branch 'develop' into feature/extractumi

  

  buehlere

  committed
  e8724f1

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• Delete sync-action.yml

  

  buehlere

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  73fedb5

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• Merge branch 'develop' into feature/extractumi

  

  buehlere

  committed
  1902b7f

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• remove poorly synced files

  

  buehlere

  committed
  0b5ff75

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• more poorly synced cleanup

  

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  committed
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Commits on Aug 9, 2023

• name change

  

  EricWilliam Buehler

  committed
  75a0cfe

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• removing old name workflow

  

  EricWilliam Buehler

  committed
  ac38f09

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• undo bad syncing

  

  buehlere

  committed
  10669ef

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• Merge branch 'develop' into feature/alignment

  

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• merge with develop

  

  buehlere

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• Delete test_data_msk.config

  

  buehlere

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  a88f7ec

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• Update main.nf

  

  buehlere

  committed
  93c3b3b

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• Merge branch 'feature/extractumi' into feature/extract_align

  

  buehlere

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• working extract to align

  

  EricWilliam Buehler

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• Update meta.yml

  

  buehlere

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  3dbcae9

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• Update meta.yml

  

  buehlere

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  824be8d

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• fixing testing

  

  EricWilliam Buehler

  committed
  0fad17d

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• Merge branch 'feature/extract_align' of https://github.com/mskcc-omics-workflows/modules into feature/extract_align

  

  EricWilliam Buehler

  committed
  8d27871

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• Update main.nf

  

  buehlere

  committed
  b9d6cdb

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• fixing md5sums?

  

  EricWilliam Buehler

  committed
  73549b2

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• update testing ymls

  

  EricWilliam Buehler

  committed
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Commits on Aug 10, 2023

• updates, still struggling with test

  

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• trying to update test

  

  EricWilliam Buehler

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• please work test

  

  EricWilliam Buehler

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• prettier

  

  EricWilliam Buehler

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