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Use github URL for Illumina format SampleSheet so -profile test works remotely #121

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Use github URL for Illumina format SampleSheet so -profile test works remotely #121

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adamrtalbot
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Fixes #103

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/demultiplex 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 5, 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/demultiplex 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/demultiplex 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!

@adamrtalbot adamrtalbot changed the base branch from master to dev June 5, 2023 09:55
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github-actions bot commented Jun 5, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d3a32ec

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '1.3.0'
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • 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
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_description - No description provided in schema for parameter: skip_tools

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-06-05 10:12:41

@drpatelh
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drpatelh commented Jun 5, 2023

Closing in favour of #123

@drpatelh drpatelh closed this Jun 5, 2023
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@maxulysse maxulysse maxulysse approved these changes

@matthdsm matthdsm Awaiting requested review from matthdsm

@edmundmiller edmundmiller Awaiting requested review from edmundmiller

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Successfully merging this pull request may close these issues.

-profile test failing due to relative path in flowcell_input.csv
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@adamrtalbot @drpatelh @maxulysse