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Nf core template merge 2.14.1 [will wait for 2.15 to merge the nf-core/tools template] #274

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Nf core template merge 2.14.1 [will wait for 2.15 to merge the nf-core/tools template] #274

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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- [ ] If necessary, also make a PR on the nf-core/nanoseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

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github-actions bot commented Sep 17, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 1514ea7

+| ✅ 222 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  15 tests had warnings |!
-| ❌  16 tests failed       |-

❌ Test failures:

  • files_exist - File not found: assets/nf-core-nanoseq_logo_light.png

  • files_exist - File must be removed: lib/NfcoreTemplate.groovy

  • files_exist - File must be removed: lib/Utils.groovy

  • files_exist - File must be removed: lib/WorkflowMain.groovy

  • nextflow_config - Config default value incorrect: params.kit is set as `` in nextflow_schema.json but is `null` in `nextflow.config`.

  • nextflow_config - Config default value incorrect: params.flowcell is set as `` in nextflow_schema.json but is `null` in `nextflow.config`.

  • nextflow_config - Config default value incorrect: params.dorado_model is set as `` in nextflow_schema.json but is `null` in `nextflow.config`.

  • nextflow_config - Config default value incorrect: params.jaffal_ref_dir is set as for_jaffal in nextflow_schema.json but is null in nextflow.config.

  • nextflow_config - Config default value incorrect: params.tracedir is set as ${params.outdir}/pipeline_info in nextflow_schema.json but is ./results/pipeline_info in nextflow.config.

  • nextflow_config - Default value from the Nextflow schema params.pipelines_testdata_base_path = true`` not found in nextflow.config.

  • schema_params - Default value for param multiqc_logo invalid: Not in pipeline parameters. Check nextflow.config.

  • schema_params - Default value for param multiqc_methods_description invalid: Not in pipeline parameters. Check nextflow.config.

  • schema_params - Default value for param pipelines_testdata_base_path invalid: Not in pipeline parameters. Check nextflow.config.

  • merge_markers - Merge marker '<<<<<<<' in /home/runner/work/nanoseq/nanoseq/docs/usage.md: <<<<<<< HEAD

  • merge_markers - Merge marker '>>>>>>>' in /home/runner/work/nanoseq/nanoseq/docs/usage.md: >>>>>>> origin/add_dorado

  • modules_config - conf/modules.config contains withName:STRINGTIE2, but the corresponding process is not present in any of the Nextflow scripts.

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.1.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • 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
  • 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!
  • schema_params - Schema param multiqc_logo not found from nextflow config
  • schema_params - Schema param multiqc_methods_description not found from nextflow config
  • schema_params - Schema param pipelines_testdata_base_path not found from nextflow config

❔ Tests ignored:

  • files_unchanged - File does not exist: assets/nf-core-nanoseq_logo_light.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-17 11:38:51

@yuukiiwa yuukiiwa changed the title Nf core template merge 2.14.1 Nf core template merge 2.14.1 [will wait for 2.15 to merge the nf-core/tools template] Sep 17, 2024
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@yuukiiwa @nf-core-bot