Fix for hidden output docs by jpcartailler · Pull Request #232 · nf-core/cutandrun

jpcartailler · 2024-02-27T19:21:10Z

Issue

There is an open <details markdown="1"> tag in the last working section (### 4.3), but no closing tag.
Then section 5 starts. Then, right after ###6.5 starts, there is dangling closing tag </details>
Then section 7 begins

Fix
Move tag to appropriate location

PR checklist

This comment contains a description of changes (with reason).
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated

3.2.1 Release Candidiate

3.2.2 Release Candidiate

github-actions · 2024-02-28T09:21:42Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit 028f027

+| ✅ 196 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   3 tests had warnings |!
-| ❌   8 tests failed       |-

Details

❌ Test failures:

files_exist - File must be removed: lib/Utils.groovy
files_exist - File must be removed: lib/WorkflowMain.groovy
files_exist - File must be removed: lib/NfcoreTemplate.groovy
files_exist - File must be removed: lib/WorkflowCutandrun.groovy
files_unchanged - .github/workflows/branch.yml does not match the template
files_unchanged - .github/workflows/linting_comment.yml does not match the template
files_unchanged - .github/workflows/linting.yml does not match the template
files_unchanged - pyproject.toml does not match the template

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 3.2.2
pipeline_todos - TODO string in WorkflowCutandrun.groovy: Optionally add in-text citation tools to this list.
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

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-cutandrun_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-cutandrun_logo_light.png
files_exist - File found: docs/images/nf-core-cutandrun_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: docs/images/nf-core-cutandrun_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
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
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
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/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.outdir= ./results
nextflow_config - Config default value correct: params.spikein_genome= K12-MG1655
nextflow_config - Config default value correct: params.clip_r1= 0
nextflow_config - Config default value correct: params.clip_r2= 0
nextflow_config - Config default value correct: params.three_prime_clip_r1= 0
nextflow_config - Config default value correct: params.three_prime_clip_r2= 0
nextflow_config - Config default value correct: params.trim_nextseq= 0
nextflow_config - Config default value correct: params.aligner= bowtie2
nextflow_config - Config default value correct: params.normalisation_c= 10000
nextflow_config - Config default value correct: params.minimum_alignment_q_score= 20
nextflow_config - Config default value correct: params.end_to_end= true
nextflow_config - Config default value correct: params.normalisation_mode= Spikein
nextflow_config - Config default value correct: params.normalisation_binsize= 50
nextflow_config - Config default value correct: params.peakcaller= seacr
nextflow_config - Config default value correct: params.use_control= true
nextflow_config - Config default value correct: params.extend_fragments= true
nextflow_config - Config default value correct: params.igg_scale_factor= 0.5
nextflow_config - Config default value correct: params.seacr_peak_threshold= 0.05
nextflow_config - Config default value correct: params.seacr_norm= non
nextflow_config - Config default value correct: params.seacr_stringent= stringent
nextflow_config - Config default value correct: params.macs2_qvalue= 0.01
nextflow_config - Config default value correct: params.macs_gsize= 2700000000.0
nextflow_config - Config default value correct: params.macs2_narrow_peak= true
nextflow_config - Config default value correct: params.macs2_broad_cutoff= 0.1
nextflow_config - Config default value correct: params.consensus_peak_mode= group
nextflow_config - Config default value correct: params.replicate_threshold= 1.0
nextflow_config - Config default value correct: params.igv_show_gene_names= true
nextflow_config - Config default value correct: params.dt_qc_bam_binsize= 500
nextflow_config - Config default value correct: params.dt_qc_corr_method= pearson
nextflow_config - Config default value correct: params.dt_heatmap_gene_beforelen= 3000
nextflow_config - Config default value correct: params.dt_heatmap_gene_bodylen= 5000
nextflow_config - Config default value correct: params.dt_heatmap_gene_afterlen= 3000
nextflow_config - Config default value correct: params.dt_heatmap_peak_beforelen= 3000
nextflow_config - Config default value correct: params.dt_heatmap_peak_afterlen= 3000
nextflow_config - Config default value correct: params.dt_calc_all_matrix= true
nextflow_config - Config default value correct: params.min_frip_overlap= 0.2
nextflow_config - Config default value correct: params.min_peak_overlap= 0.2
nextflow_config - Config default value correct: params.igv_sort_by_groups= true
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.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
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 - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-cutandrun_logo_light.png matches the template
files_unchanged - docs/images/nf-core-cutandrun_logo_light.png matches the template
files_unchanged - docs/images/nf-core-cutandrun_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
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
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_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (290 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: awstest.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: awsfulltest.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: release-announcements.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' contains report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
multiqc_config - 'assets/multiqc_config.yml' contains report_comment
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.13
Run at 2024-02-28 09:21:03

chris-cheshire · 2024-04-26T09:07:25Z

Hi @jpcartailler, sorry for taking so long to get to this, I have been away on Paternity leave. Could you fix the tests and I can merge?

jpcartailler · 2024-04-26T13:06:47Z

Thanks @chris-cheshire and no worries, being a dad is way more important.

I'm a little puzzled by the errors to be honest. I was just modifying two .md files, but see errors related to the following:

[files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: lib/Utils.groovy
    [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: lib/WorkflowMain.groovy
    [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: lib/NfcoreTemplate.groovy
    [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: lib/WorkflowCutandrun.groovy
    [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - .github/workflows/branch.yml does not match the template
    [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - .github/workflows/linting_comment.yml does not match the template
    [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - .github/workflows/linting.yml does not match the template
    [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - pyproject.toml does not match the template

Any thoughts or guidance? TY

chris-cheshire · 2024-04-29T10:34:54Z

Damn i think I need to upgrade the pipeline to pass the new nf-core tools spec. Bear with me, I will update the pipeline and then you will need to pull from dev

jpcartailler · 2024-05-07T19:00:15Z

Thanks @chris-cheshire - is there anything for me to try yet?

chris-cheshire · 2024-05-14T08:49:55Z

Not yet no, this needs quite a large update I am afraid. Nf-core have removed all the groovy libs in favour of plugins so its a substantial code change

chris-cheshire and others added 4 commits October 25, 2023 11:31

Merge pull request nf-core#214 from nf-core/dev

2727de3

3.2.1 Release Candidiate

Merge pull request nf-core#230 from nf-core/dev

6e1125d

3.2.2 Release Candidiate

Updated CHANGELOG.md as per instructions

9e3d0af

Fixed output docs (section 5 and 6 were hidden)

028f027

chris-cheshire approved these changes Nov 18, 2025

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Fix for hidden output docs#232

Fix for hidden output docs#232
jpcartailler wants to merge 4 commits intonf-core:devfrom
jpcartailler:jp-docs-fix

jpcartailler commented Feb 27, 2024

Uh oh!

github-actions bot commented Feb 28, 2024 •

edited

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❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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chris-cheshire commented Apr 26, 2024

Uh oh!

jpcartailler commented Apr 26, 2024

Uh oh!

chris-cheshire commented Apr 29, 2024

Uh oh!

jpcartailler commented May 7, 2024

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chris-cheshire commented May 14, 2024

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jpcartailler commented Feb 27, 2024

PR checklist

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github-actions bot commented Feb 28, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

chris-cheshire commented Apr 26, 2024

Uh oh!

jpcartailler commented Apr 26, 2024

Uh oh!

chris-cheshire commented Apr 29, 2024

Uh oh!

jpcartailler commented May 7, 2024

Uh oh!

chris-cheshire commented May 14, 2024

Uh oh!

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github-actions bot commented Feb 28, 2024 •

edited

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`nf-core lint` overall result: Failed ❌