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Simplify sentieon test license server usage #1242

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merged 13 commits into from Sep 18, 2023
Merged

Simplify sentieon test license server usage #1242

merged 13 commits into from Sep 18, 2023

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maxulysse
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Replace #1237 and #1238

Idea is to move it to configs nf-core/configs#551
To allow better control on how we can deal with this test license server for all nf-core pipelines / modules that needs it.
Plus being more future proof as we can modify configs without having to modify pipelines/modules

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github-actions bot commented Sep 18, 2023 •
edited

nf-core lint overall result: Passed ✅

Posted for pipeline commit c12ed5b

+| ✅ 143 tests passed       |+
#| ❔   9 tests were ignored |#

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-18 14:15:50

maxulysse
maxulysse commented Sep 18, 2023
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maxulysse
maxulysse commented Sep 18, 2023
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asp8200
asp8200 reviewed Sep 18, 2023
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tests/config/tags.yml
@@ -138,7 +138,7 @@ sentieon/bwamem:
- modules/nf-core/sentieon/bwamem/main.nf
- subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/main.nf
- tests/csv/3.0/fastq_single.csv
- tests/test_aligner_sentieon_bwamem.yml
- tests/test_sentieon_aligner_bwamem.yml
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The aligner is called "sentieon bwamem" hence the order of the words in the filename.

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yeah, I know, but when renamed this way all the sentieon tests files are nicely grouped together

maxulysse
maxulysse commented Sep 18, 2023
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@maxulysse maxulysse merged commit 647b664 into dev Sep 18, 2023
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@maxulysse maxulysse deleted the sentieon-license-fixing3 branch September 18, 2023 14:29
FriederikeHanssen
FriederikeHanssen reviewed Sep 18, 2023
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How come the new parameter is not part of the schema? When is it supposed to be used? For anyone, just for testing?

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How come the new parameter is not part of the schema? When is it supposed to be used? For anyone, just for testing?

because it's a params from configs: nf-core/configs#551

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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@asp8200 asp8200 asp8200 approved these changes

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@maxulysse @FriederikeHanssen @asp8200