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Update Sentieon Docs #1579

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Update Sentieon Docs #1579

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@edmundmiller edmundmiller commented Jul 1, 2024 •
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Waiting until we get #1380 up and running.

@edmundmiller edmundmiller self-assigned this Jul 1, 2024
@edmundmiller edmundmiller added this to the 3.5 milestone Jul 1, 2024
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c332140

+| ✅ 200 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings
  • modules_config - modules_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-19 21:51:19

@edmundmiller edmundmiller mentioned this pull request Jul 16, 2024
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@FriederikeHanssen FriederikeHanssen removed this from the 3.5 milestone Aug 19, 2024
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FriederikeHanssen previously approved these changes Aug 20, 2024
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Sentieon server is up and running so I think we can merge this.

I have only tested out adding a env config

env {
    SENTIEON_LICENSE = 'IP:PORT'
}

without the secrets, but this works great

@edmundmiller edmundmiller marked this pull request as ready for review August 21, 2024 22:40
@maxulysse
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Can you update CHANGELOG?

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@maxulysse As you wish!

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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@edmundmiller @maxulysse @FriederikeHanssen