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Important! Template update for nf-core/tools v2.13.1 #3

Merged
merged 14 commits into from
Mar 15, 2024
Merged

Important! Template update for nf-core/tools v2.13.1 #3

merged 14 commits into from
Mar 15, 2024

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Version 2.13.1 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-2.13.1 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 v2.13.1 release page.

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github-actions bot commented Mar 14, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 23f53ab

+| ✅ 155 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗  40 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 0.3.1
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • 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 test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • system_exit - System.exit in main.nf: System.exit(1) [line 44]
  • system_exit - System.exit in main.nf: System.exit(1) [line 46]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 114]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 121]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 128]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 142]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 152]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 157]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 170]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 186]
  • system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 195]
  • system_exit - System.exit in WorkflowOncoanalyser.groovy: System.exit(1) [line 62]
  • system_exit - System.exit in Processes.groovy: System.exit(1) [line 33]
  • system_exit - System.exit in Processes.groovy: System.exit(1) [line 49]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 29]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 40]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 48]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 56]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 64]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 69]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 117]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 193]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 205]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 213]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 220]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 228]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 243]
  • system_exit - System.exit in Utils.groovy: System.exit(1) [line 337]

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-15 04:54:59

@scwatts scwatts added this to the Release 1.0.0 milestone Mar 15, 2024
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scwatts commented Mar 15, 2024

Force push to correct previous commit

@scwatts scwatts force-pushed the nf-core-template-merge-2.13.1 branch from 20ad49e to 45ce699 Compare March 15, 2024 03:29
@scwatts scwatts merged commit 47d551b into dev Mar 15, 2024
4 checks passed
@scwatts scwatts deleted the nf-core-template-merge-2.13.1 branch March 15, 2024 05:05
@scwatts scwatts mentioned this pull request Mar 15, 2024
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@scwatts scwatts scwatts approved these changes

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