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Updates to yaml and references + formatting #176

Merged
merged 16 commits into from
Nov 23, 2023
Merged

Updates to yaml and references + formatting #176

merged 16 commits into from
Nov 23, 2023

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DLBPointon
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Formatting fixes

Yaml value update
References to values updated
Some channels are refactors because of this
Moved some tuple creation to the yaml_input subworkflow, this makes more sense in that this subworkflow is supposed to initiate everything.

@DLBPointon DLBPointon added the enhancement New feature or request label Nov 22, 2023
@DLBPointon DLBPointon added this to the Release 1 milestone Nov 22, 2023
@DLBPointon DLBPointon self-assigned this Nov 22, 2023
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github-actions bot commented Nov 22, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 22dacae

+| ✅ 127 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: '1.0.2'
  • pipeline_todos - TODO string in methods_description_template.yml: ## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • system_exit - System.exit in WorkflowTreeval.groovy: System.exit(1) [line 17]

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-treeval_logo_dark.png
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • 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 ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-treeval_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/treeval/treeval/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-11-23 17:35:30

@DLBPointon
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Closes #178, #168

@DLBPointon DLBPointon requested review from priyanka-surana, yumisims and weaglesBio and removed request for priyanka-surana November 23, 2023 11:01
@DLBPointon DLBPointon added the Release 1.1 Issues to be resolved for minor release 1.1 label Nov 23, 2023
This was linked to issues Nov 23, 2023
Generalise yaml values #168
Closed
CAT_CAT & FASTK_FASTK in KMER causing naming issues #178
Closed
@DLBPointon DLBPointon linked an issue Nov 23, 2023 that may be closed by this pull request
Adjust images again #169
Closed
@DLBPointon DLBPointon linked an issue Nov 23, 2023 that may be closed by this pull request
REQUEST: Container size into summary file #143
Closed
@DLBPointon DLBPointon linked an issue Nov 23, 2023 that may be closed by this pull request
Update DOCS #180
Closed
weaglesBio
weaglesBio approved these changes Nov 23, 2023
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Looks good generally. Is longreads_new the clearest descriptive name option? Would it help to include channel in the name.

@DLBPointon DLBPointon linked an issue Nov 23, 2023 that may be closed by this pull request
Re-organise and annotate .config files #98
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Looks good generally. Is longreads_new the clearest descriptive name option? Would it help to include channel in the name.

Ah, they were the testing variables. I'll fix those now.

@DLBPointon DLBPointon merged commit 8b89ad4 into dev Nov 23, 2023
6 checks passed
@DLBPointon DLBPointon deleted the dp24_yaml_update branch November 23, 2023 17:52
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@weaglesBio weaglesBio weaglesBio approved these changes

@yumisims yumisims Awaiting requested review from yumisims

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@DLBPointon DLBPointon

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enhancement New feature or request Release 1.1 Issues to be resolved for minor release 1.1
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@DLBPointon @weaglesBio