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Important! Template update for nf-core/tools v2.12 #257

Merged
merged 8 commits into from
Jan 30, 2024
Merged

Important! Template update for nf-core/tools v2.12 #257

merged 8 commits into from
Jan 30, 2024

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Version 2.12 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-2.12 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 v2.12 release page.

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github-actions bot commented Jan 29, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit bb72957

+| ✅ 147 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   6 tests had warnings |!
-| ❌   1 tests failed       |-

❌ Test failures:

  • files_unchanged - assets/sendmail_template.txt does not match the template

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • 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

❔ Tests ignored:

  • 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/WorkflowMain.groovy
  • files_unchanged - File does not exist: 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 2.12
  • Run at 2024-01-29 21:47:35

@drpatelh drpatelh mentioned this pull request Jan 29, 2024
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adamrtalbot
adamrtalbot requested changes Jan 29, 2024
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Seems to have rolled back all subworkflow changes. We need to fix that before we can merge anything.

subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config Show resolved Hide resolved
subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml Outdated Show resolved Hide resolved
@drpatelh drpatelh merged commit 7018fc3 into dev Jan 30, 2024
38 of 39 checks passed
@adamrtalbot adamrtalbot deleted the nf-core-template-merge-2.12 branch January 30, 2024 10:34
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@drpatelh drpatelh drpatelh left review comments

@adamrtalbot adamrtalbot adamrtalbot approved these changes

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