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Template update #6

Merged
merged 40 commits into from
Aug 11, 2023
Merged

Template update #6

merged 40 commits into from
Aug 11, 2023

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muffato
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@muffato muffato commented Jul 15, 2023

Closes #4
I've updated the pipeline template from 2.5 to 2.8.

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
  • 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).

@muffato muffato added the maintain Tasks to keep pipelines up to date label Jul 15, 2023
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github-actions bot commented Jul 15, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 02a0b32

+| ✅ 131 tests passed       |+
#| ❔  22 tests were ignored |#

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: assets/nf-core-ensemblgenedownload_logo_light.png
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: docs/images/nf-core-ensemblgenedownload_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-ensemblgenedownload_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-ensemblgenedownload_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-ensemblgenedownload_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-ensemblgenedownload_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/ensemblgenedownload/ensemblgenedownload/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-08-11 07:08:15

@muffato muffato changed the base branch from main to dev July 15, 2023 22:30
@muffato muffato marked this pull request as ready for review July 16, 2023 08:08
@muffato muffato added enhancement Improvement of the existing features and removed enhancement Improvement of the existing features labels Jul 16, 2023
@muffato muffato requested a review from priyanka-surana July 17, 2023 08:43
priyanka-surana
priyanka-surana suggested changes Aug 1, 2023
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Mostly need more clarity for input parameters for ToL and non-ToL assemblies. The other comments are similar to insdcdownload.

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@muffato muffato mentioned this pull request Aug 4, 2023
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@muffato muffato linked an issue Aug 4, 2023 that may be closed by this pull request
Add CI tests on the farm #7
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muffato commented Aug 4, 2023

I've also added the yml files to run this pipeline through Tower on the farm

This was referenced Aug 4, 2023
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priyanka-surana
priyanka-surana approved these changes Aug 11, 2023
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LGTM 👍🏼 Thanks for making the changes.

@muffato muffato merged commit 2cf5ba2 into dev Aug 11, 2023
@muffato muffato deleted the template_update branch August 11, 2023 09:45
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@priyanka-surana priyanka-surana priyanka-surana approved these changes

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Update pipeline template Add CI tests on the farm
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