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Update usage.md #94

Merged
merged 2 commits into from
Feb 21, 2025
Merged

Update usage.md #94

merged 2 commits into from
Feb 21, 2025

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DLBPointon
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The documentation was out of date for the current running method e.g need for samplesheet and changes to reflect reads needing to be a list now.

Effects #93

@DLBPointon DLBPointon added documentation Improvements or additions to documentation Release 1 labels Feb 21, 2025
@DLBPointon DLBPointon self-assigned this Feb 21, 2025
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github-actions bot commented Feb 21, 2025 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a3cfa52

+| ✅ 112 tests passed       |+
#| ❔  35 tests were ignored |#
!| ❗  17 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: lib/WorkflowAscc.groovy
  • nextflow_config - Config manifest.version should end in dev: '0.1.0'
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • 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 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 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 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 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
  • schema_lint - Schema $schema should be http://json-schema.org/draft-07/schema
    Found https://json-schema.org/draft-07/schema

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-ascc_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-ascc_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-ascc_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: lib/nfcore_external_java_deps.jar
  • files_exist - File is ignored: lib/NfcoreSchema.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • nextflow_config - Config variable ignored: params.show_hidden_params
  • nextflow_config - Config variable ignored: params.schema_ignore_params
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.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/branch.yml
  • 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.html
  • files_unchanged - File ignored due to lint config: assets/nf-core-ascc_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-ascc_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-ascc_logo_dark.png
  • files_unchanged - File does not exist: lib/nfcore_external_java_deps.jar
  • files_unchanged - File does not exist: lib/NfcoreSchema.groovy
  • files_unchanged - File does not exist: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/ascc/ascc/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2025-02-21 11:44:17

@DLBPointon DLBPointon changed the base branch from dev to dp24_schema_update February 21, 2025 13:47
@DLBPointon DLBPointon merged commit b279b15 into dp24_schema_update Feb 21, 2025
1 of 4 checks passed
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