remove broken sync to dev workflow

[apsteinberg]

kentsislab/proteomegenerator3 pull request

Remove sync to dev workflow (breaks on fork)

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fd931ba

+| ✅  39 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

• readme - README did not have a Nextflow minimum version badge.
• readme - README did not have an nf-core template version badge.
• readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).

❔ Tests ignored:

• files_exist - files_exist
• nextflow_config - nextflow_config
• nf_test_content - nf_test_content
• files_unchanged - File ignored due to lint config: .prettierrc.yml
• files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
• files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: .github/workflows/linting_comment.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File ignored due to lint config: assets/email_template.txt
• files_unchanged - File ignored due to lint config: assets/nf-core-proteomegenerator3_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-proteomegenerator3_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-proteomegenerator3_logo_dark.png
• files_unchanged - File ignored due to lint config: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
• actions_nf_test - '.github/workflows/nf-test.yml' not found
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/proteomegenerator3/proteomegenerator3/.github/workflows/awstest.yml
• actions_schema_validation - actions_schema_validation
• rocrate_readme_sync - rocrate_readme_sync

✅ Tests passed:

• files_unchanged - .gitattributes matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/workflows/branch.yml matches the template
• files_unchanged - assets/email_template.html matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• pipeline_todos - No TODO strings found
• pipeline_if_empty_null - No ifEmpty(null) strings found
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - assets/multiqc_config.yml found and not ignored.
• multiqc_config - assets/multiqc_config.yml contains report_section_order
• multiqc_config - assets/multiqc_config.yml contains export_plots
• multiqc_config - assets/multiqc_config.yml contains report_comment
• multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
• multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - DIAMOND_BLASTP found in conf/modules.config and Nextflow scripts.
• modules_config - KENTSISLAB_PROTEOMEGENERATOR3 found in conf/modules.config and Nextflow scripts.
• modules_config - GFFREAD found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_READS found in conf/modules.config and Nextflow scripts.
• modules_config - BAMBU_READCLASSES found in conf/modules.config and Nextflow scripts.
• modules_config - BAMBU_MERGE found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.3.2

Run details

• nf-core/tools version 3.3.2
• Run at 2025-11-15 03:15:57