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Important! Template update for nf-core/tools v2.11 #242

Merged
merged 3 commits into from
Jan 5, 2024
Merged

Important! Template update for nf-core/tools v2.11 #242

merged 3 commits into from
Jan 5, 2024

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nf-core-bot
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Version 2.11 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-2.11 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/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v2.11 release page.

@drpatelh drpatelh added this to the 1.12.0 milestone Jan 3, 2024
@drpatelh drpatelh mentioned this pull request Jan 4, 2024
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github-actions bot commented Jan 5, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit c642adf

+| ✅ 134 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 1.11.0
  • 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 meta.yml: #Add a description of the subworkflow and list keywords
  • pipeline_todos - TODO string in meta.yml: #Add a list of the modules and/or subworkflows used in the subworkflow
  • pipeline_todos - TODO string in meta.yml: #List all of the channels used as input with a description and their structure
  • pipeline_todos - TODO string in meta.yml: #List all of the channels used as output with a descriptions and their structure

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: conf/modules.config
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowFetchngs.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/nfcore_external_java_deps.jar
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: lib/nfcore_external_java_deps.jar
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-05 10:54:11

adamrtalbot
adamrtalbot approved these changes Jan 5, 2024
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lgtm

@drpatelh drpatelh merged commit 176b130 into dev Jan 5, 2024
8 checks passed
@maxulysse maxulysse deleted the nf-core-template-merge-2.11 branch January 9, 2024 12:46
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

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