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Template update nf-core tools v2.8 #256

Merged
merged 14 commits into from
May 4, 2023
Merged

Template update nf-core tools v2.8 #256

merged 14 commits into from
May 4, 2023

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ggabernet
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Template update nf-core tools v2.8

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/airrflow branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented May 1, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d1888ab

+| ✅ 159 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-03 18:30:43

FriederikeHanssen
FriederikeHanssen approved these changes May 2, 2023
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README.md

## Credits

nf-core/airrflow was written by [Gisela Gabenet](https://github.com/ggabernet), [Susanna Marquez](https://github.com/ssnn-airr), [Alexander Peltzer](@apeltzer) and [Simon Heumos](@subwaystation).
nf-core/airrflow was written by [Gisela Gabernet](https://github.com/ggabernet), [Susanna Marquez](https://github.com/ssnn-airr), [Alexander Peltzer](@apeltzer) and [Simon Heumos](@subwaystation).
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🙈

nextflow.config Outdated
charliecloud.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
docker.enabled = true
// docker.registry = 'quay.io'
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Is it still not working with the merged modules? :(

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This will start to break as new modules come out. Better to update the existing modules. The basic gist is you need to update the container to the full URI:

container "ubuntu:20.04"

to

container "docker.io/library/ubuntu:20.04

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ah ok got it just fixed that. So when "quay.io/" is present that does not break things. I was wondering this because none of the modules were yet updated in this respect, but it works like that

conf/igenomes.config
@@ -0,0 +1,440 @@
/*
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Is it right, that the whole file is new? You didn't have an igenomes file before?

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no, because it does not use igenomes but pull specific reference data for BCR / TCR

mashehu
mashehu approved these changes May 3, 2023
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README.md Outdated Show resolved Hide resolved
@ggabernet ggabernet merged commit e5ccb67 into nf-core:dev May 4, 2023
@ggabernet ggabernet deleted the merging-template-updates branch November 27, 2024 01:11
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@adamrtalbot adamrtalbot adamrtalbot left review comments

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@mashehu mashehu mashehu approved these changes

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@ggabernet @mashehu @FriederikeHanssen @adamrtalbot @nf-core-bot