Add Mermaid diagram #268

adamrtalbot · 2024-02-02T11:13:42Z

Add flow diagram written in Mermaid.

PR checklist

github-actions · 2024-02-02T11:14:58Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit c8ec03b

+| ✅ 150 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   6 tests had warnings |!

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yml
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files_exist - File not found: .github/workflows/awstest.yml
files_exist - File not found: .github/workflows/awsfulltest.yml
files_exist - File not found: lib/WorkflowFetchngs.groovy
nextflow_config - Config manifest.version should end in dev: 1.12.0

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: lib/NfcoreTemplate.groovy
files_exist - File is ignored: lib/Utils.groovy
files_exist - File is ignored: lib/WorkflowMain.groovy
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File does not exist: lib/NfcoreTemplate.groovy
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/fetchngs/fetchngs/.github/workflows/awstest.yml
multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

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nextflow_config - Config variable found: manifest.name
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nextflow_config - Config variable found: timeline.enabled
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nextflow_config - Config variable found: timeline.file
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nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
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nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
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nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.sample_mapping_fields= experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description
nextflow_config - Config default value correct: params.nf_core_rnaseq_strandedness= auto
nextflow_config - Config default value correct: params.download_method= ftp
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
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files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/nf-core-fetchngs_logo_light.png matches the template
files_unchanged - docs/images/nf-core-fetchngs_logo_light.png matches the template
files_unchanged - docs/images/nf-core-fetchngs_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (150 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
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: cloud_tests_small.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: cloud_tests_full.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.12.1
Run at 2024-02-20 12:48:41

README.md

adamrtalbot · 2024-02-02T11:17:17Z

We can play with themes and formats, take a look at the docs and see if there's any that take are close to the nf-core theme.

https://mermaid.js.org/config/directives.html#declaring-directives

maxulysse · 2024-02-02T12:26:57Z

Looking super nice

drpatelh

Noice!

drpatelh · 2024-02-18T11:56:09Z

@nf-core-bot fix linting

drpatelh · 2024-02-18T11:59:13Z

Any idea why the confirm-pass is failing here @adamrtalbot even though all tests have passed?

drpatelh · 2024-02-18T12:38:22Z

Will also need to change the diagram to reflect the changes in #277

i.e. revert to making FTP default download method and renaming --force_ftp_download to --force_aspera_download.

Is there a way we can put the parameters above the edges rather than in-line? Tricky to see the dashes. Don't worry if not.

README.md

maxulysse · 2024-02-19T09:01:50Z

pushed some changes to re-trigger the tests

adamrtalbot added 2 commits February 2, 2024 11:13

Add Mermaid diagram

b35e947

Correct CHANGELOG

e5daf3a

maxulysse reviewed Feb 2, 2024

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Change theme to Forest

fb324b8

maxulysse reviewed Feb 2, 2024

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adamrtalbot added 6 commits February 2, 2024 11:19

Trying some themes

bece634

Remove backticks|

26ba758

Remove some theme stuff

7b69bce

pulling more stuff out of the mermaid

0e18e7e

Approximate nf-core theme (attempt 1)

f94c742

Style updates to Mermaid

ddf7e3c

adamrtalbot and others added 2 commits February 2, 2024 16:01

Remove theme stuff because it doesn't work on Github Dark mode

64a40cf

Merge branch 'dev' into add_flow_diagram

f9101d7

drpatelh approved these changes Feb 18, 2024

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[automated] Fix linting with Prettier

ba7d804

maxulysse reviewed Feb 19, 2024

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Apply suggestions from code review

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Update README.md

c8ec03b

maxulysse approved these changes Feb 20, 2024

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drpatelh merged commit ad81106 into nf-core:dev Feb 20, 2024
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Add Mermaid diagram #268

Add Mermaid diagram #268

adamrtalbot commented Feb 2, 2024 •

edited

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github-actions bot commented Feb 2, 2024 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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adamrtalbot commented Feb 2, 2024

maxulysse commented Feb 2, 2024

drpatelh left a comment

drpatelh commented Feb 18, 2024

drpatelh commented Feb 18, 2024

drpatelh commented Feb 18, 2024

maxulysse commented Feb 19, 2024

Add Mermaid diagram #268

Add Mermaid diagram #268

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adamrtalbot commented Feb 2, 2024 • edited Loading

PR checklist

github-actions bot commented Feb 2, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

adamrtalbot commented Feb 2, 2024

maxulysse commented Feb 2, 2024

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drpatelh commented Feb 18, 2024

drpatelh commented Feb 18, 2024

drpatelh commented Feb 18, 2024

maxulysse commented Feb 19, 2024

adamrtalbot commented Feb 2, 2024 •

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github-actions bot commented Feb 2, 2024 •

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`nf-core lint` overall result: Passed ✅ ⚠️