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[DOC] More structure plus add everything to TOC #85

Merged
merged 3 commits into from
Mar 7, 2022
Merged

[DOC] More structure plus add everything to TOC #85

merged 3 commits into from
Mar 7, 2022

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jpfeuffer
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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/quantms 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).
  • 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).

@jpfeuffer jpfeuffer changed the title [DOC ]More structure plus add everything to TOC [DOC] More structure plus add everything to TOC Mar 7, 2022
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github-actions bot commented Mar 7, 2022 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 9f7004d

+| ✅ 116 tests passed       |+
#| ❔   6 tests were ignored |#
-| ❌  33 tests failed       |-

❌ Test failures:

  • files_exist - File not found: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_exist - File not found: .github/ISSUE_TEMPLATE/feature_request.yml
  • files_exist - File not found: assets/nf-core-quantms_logo_light.png
  • files_exist - File not found: docs/images/nf-core-quantms_logo_light.png
  • files_exist - File not found: docs/images/nf-core-quantms_logo_dark.png
  • files_exist - File not found: docs/usage.md
  • files_exist - File must be removed: .github/ISSUE_TEMPLATE/bug_report.md
  • files_exist - File must be removed: .github/ISSUE_TEMPLATE/feature_request.md
  • files_exist - File must be removed: docs/images/nf-core-quantms_logo.png
  • files_unchanged - .gitattributes does not match the template
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/config.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - assets/sendmail_template.txt does not match the template
  • files_unchanged - lib/NfcoreSchema.groovy does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • files_unchanged - assets/multiqc_config.yaml does not match the template
  • actions_ci - '.github/workflows/ci.yml' does not check minimum NF version
  • schema_params - Default value for param root_folder invalid: String should not be set to ''
  • schema_params - Default value for param local_input_type invalid: String should not be set to ''
  • schema_params - Default value for param peakpicking_ms_levels invalid: String should not be set to ''
  • schema_params - Default value for param label invalid: String should not be set to ''
  • schema_params - Default value for param instrument invalid: String should not be set to ''
  • schema_params - Default value for param luciphor_neutral_losses invalid: String should not be set to ''
  • schema_params - Default value for param luciphor_decoy_mass invalid: Does not look like a number (float): ''
  • schema_params - Default value for param luciphor_decoy_neutral_losses invalid: String should not be set to ''
  • schema_params - Default value for param allow_unmatched invalid: String should not be set to false
  • schema_params - Default value for param annotate_file_origin invalid: Schema default (True) does not match the config default (false)
  • schema_params - Default value for param protein_fdr invalid: Schema default (False) does not match the config default (true)
  • schema_params - Default value for param include_all invalid: Schema default (False) does not match the config default (true)
  • schema_params - Default value for param transfer_ids invalid: String should not be set to false
  • schema_params - Default value for param ref_condition invalid: String should not be set to ''
  • schema_params - Default value for param ptxqc_report_layout invalid: String should not be set to ''

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/feature_request.yml
  • files_unchanged - File does not exist: assets/nf-core-quantms_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-quantms_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-quantms_logo_dark.png

✅ Tests passed:

Run details

  • nf-core/tools version 2.2
  • Run at 2022-03-07 12:10:07

@jpfeuffer jpfeuffer merged commit 7283320 into bigbio:readthedocs Mar 7, 2022
ypriverol added a commit that referenced this pull request Mar 21, 2023
@ypriverol
Merge pull request #85 from nf-core/dev
0682a4b 
Add release date and Zenodo DOI for version 1.1.0
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@jpfeuffer