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Fix some template sync errors #244

Merged
merged 2 commits into from
Sep 14, 2022
Merged

Fix some template sync errors #244

merged 2 commits into from
Sep 14, 2022

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ewels
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@ewels ewels commented Sep 14, 2022 •
edited by njspix
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Manually checking standard template files and fixing sync errors.

  • GitHub workflows
  • lib/*

I made a new pipeline with nf-core create with the latest release and then was checking core files with diff.

I think that some work is still needed for lib:

$ for f in lfor f in lib/*; do
>  delta ../methylseq-template-temp/nf-core-methylseq/$f $f
>  done
error: Could not access '../methylseq-template-temp/nf-core-methylseq/lib/Checks.groovy'
error: Could not access '../methylseq-template-temp/nf-core-methylseq/lib/Completion.groovy'

 (mode -x)
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
error: Could not access '../methylseq-template-temp/nf-core-methylseq/lib/Workflow.groovy'

I think Utils and Checks were once the same, some functions such as `checkCondaChannels´ are duplicated for instance.

Not entirely sure what should be there as it's been customised and what should be removed. If anyone else fancies having a stab at it that would be fab 👍🏻

This PR can be merged as-is, I'm fairly happy with the workflow fixes.

Phil

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github-actions bot commented Sep 14, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d9ea338

+| ✅ 153 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

✅ Tests passed:

Run details

  • nf-core/tools version 2.5.1
  • Run at 2022-09-14 12:27:34

edmundmiller
edmundmiller approved these changes Sep 14, 2022
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So weird those didn't get picked up...

@ewels ewels merged commit eb93ad5 into nf-core:dsl2 Sep 14, 2022
@ewels ewels deleted the dsl2 branch September 14, 2022 13:40
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ewels commented Sep 14, 2022

So weird those didn't get picked up...

The newer code using tower-action was in there already, it was just that the older code hadn't been deleted. It was customised from the old template, so the sync wouldn't have been able to delete it automatically.

@ewels ewels restored the dsl2 branch September 14, 2022 13:41
@edmundmiller edmundmiller added this to the 2.0.0 milestone Nov 4, 2022
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@edmundmiller edmundmiller edmundmiller approved these changes

@njspix njspix Awaiting requested review from njspix

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@ewels @edmundmiller