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Remove globs from ecr profile #228

Merged
merged 1 commit into from
Jun 1, 2023
Merged

Remove globs from ecr profile #228

merged 1 commit into from
Jun 1, 2023

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adamrtalbot
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Removes globs from ECR profile which means they will be correctly found if using an alias. i.e.,:

include { TOOL as SUBTOOL } from file.nf

will match:

withName: TOOL

or

withName: .*SUBTOOL

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/scrnaseq 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 Jun 1, 2023

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @adamrtalbot,

It looks like this pull-request is has been made against the adamrtalbot/scrnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the adamrtalbot/scrnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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

Posted for pipeline commit f88f8d3

+| ✅ 157 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '2.3.1'
  • system_exit - System.exit in WorkflowScrnaseq.groovy: System.exit(1) [line 18]

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-01 10:58:54

@adamrtalbot adamrtalbot changed the base branch from master to dev June 1, 2023 10:57
drpatelh
drpatelh approved these changes Jun 1, 2023
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LGTM!

@adamrtalbot adamrtalbot merged commit 113fe82 into nf-core:dev Jun 1, 2023
@adamrtalbot adamrtalbot deleted the remove_globs_from_ecr_profile branch June 1, 2023 11:22
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@maxulysse maxulysse maxulysse approved these changes

@drpatelh drpatelh drpatelh approved these changes

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@adamrtalbot @maxulysse @drpatelh