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Merging template 2.12 #126

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Merging template 2.12 #126

wants to merge 3 commits into from

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JoseEspinosa
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @JoseEspinosa,

It looks like this pull-request is has been made against the JoseEspinosa/nf-core-proteinfold master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the JoseEspinosa/nf-core-proteinfold dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@JoseEspinosa JoseEspinosa changed the base branch from master to dev January 29, 2024 22:09
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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 ac2f8df

+| ✅ 176 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗  11 tests had warnings |!
-| ❌  11 tests failed       |-

❌ Test failures:

  • files_exist - File must be removed: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config default value incorrect: params.alphafold2_model_preset is set as monomer_ptm in nextflow_schema.json but is monomer in nextflow.config.
  • nextflow_config - Config default value incorrect: params.uniref30_colabfold_link is set as http://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2103.tar.gz in nextflow_schema.json but is https://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2202.tar.gz in nextflow.config.
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/nf-core-proteinfold_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-proteinfold_logo_light.png does not match the template
  • files_unchanged - docs/images/nf-core-proteinfold_logo_dark.png does not match the template

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowProteinfold.groovy
  • pipeline_todos - TODO string in check_samplesheet.py: Update the script to check the samplesheet
  • pipeline_todos - TODO string in check_samplesheet.py: Update the check_samplesheet function
  • pipeline_todos - TODO string in check_samplesheet.py: Update the column names for the input samplesheet
  • 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in WorkflowAlphafold2.groovy: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
  • 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:

✅ Tests passed:

Run details

  • nf-core/tools version 2.12
  • Run at 2024-01-29 22:09:00

@JoseEspinosa JoseEspinosa deleted the merging-template-2.12 branch January 29, 2024 22:17
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@JoseEspinosa @nf-core-bot