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Important! Template update for nf-core/tools v2.9 #132

Merged
merged 9 commits into from
Aug 24, 2023
Merged

Important! Template update for nf-core/tools v2.9 #132

merged 9 commits into from
Aug 24, 2023

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nf-core-bot
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Version 2.9 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.9 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/developers/sync.

For more information about this release of nf-core/tools, please see the v2.9 release page.

@edmundmiller edmundmiller self-assigned this Aug 21, 2023
@edmundmiller edmundmiller added this to the 1.4.0 milestone Aug 21, 2023
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github-actions bot commented Aug 22, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6cdeafc

+| ✅ 154 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • 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 preferred 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 2.9
  • Run at 2023-08-23 17:29:35

matthdsm
matthdsm reviewed Aug 23, 2023
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CITATIONS.md Outdated Show resolved Hide resolved
assets/schema_input.json
@@ -7,7 +7,7 @@
"items": {
"type": "object",
"properties": {
"flowcell": {
"id": {
"type": "string",
"description": "Flowcell ID",
"pattern": "^\\S+$",
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⏬ The error message still needs to be fixed

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Which error message?

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Gonna merge, we can follow up in another PR if necessary!

assets/schema_input.json Show resolved Hide resolved
edmundmiller and others added 2 commits August 23, 2023 12:27
@edmundmiller @matthdsm
chore: Fix merge error with fastqc
6305646 
Co-authored-by: matthdsm <matthdsm@users.noreply.github.com>
@edmundmiller @maxulysse
fix: Remove fasta check all together
6cdeafc 
Co-authored-by: maxulysse <maxulysse@users.noreply.github.com>
@edmundmiller edmundmiller mentioned this pull request Aug 23, 2023
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maxulysse
maxulysse approved these changes Aug 24, 2023
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LGTM

@edmundmiller edmundmiller merged commit aefefde into dev Aug 24, 2023
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@edmundmiller edmundmiller deleted the nf-core-template-merge-2.9 branch August 24, 2023 13:10
This was referenced Oct 16, 2023
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@maxulysse maxulysse maxulysse approved these changes

@edmundmiller edmundmiller Awaiting requested review from edmundmiller

@matthdsm matthdsm Awaiting requested review from matthdsm

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@nf-core-bot @maxulysse @matthdsm @edmundmiller