Release 3.0.0 by maxulysse · Pull Request #16 · maxulysse/compile-latex

maxulysse · 2026-04-13T15:57:11Z

No description provided.

github-actions · 2026-04-16T14:15:47Z

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

Posted for pipeline commit e7ce6ca

+| ✅ 137 tests passed       |+
#| ❔  38 tests were ignored |#
!| ❗   1 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 3.0.0

❔ Tests ignored:

files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/ci.yml
files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/email_template.html
files_exist - File is ignored: assets/email_template.txt
files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: assets/nf-core-compile-latex_logo_light.png
files_exist - File is ignored: assets/sendmail_template.txt
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: conf/modules.config
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: docs/README.md
files_exist - File is ignored: docs/images/nf-core-compile-latex_logo_dark.png
files_exist - File is ignored: docs/images/nf-core-compile-latex_logo_light.png
files_exist - File is ignored: docs/output.md
files_exist - File is ignored: docs/usage.md
nf_test_content - nf_test_content
files_unchanged - File does not exist: CODE_OF_CONDUCT.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/workflows/linting_comment.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File does not exist: assets/email_template.html
files_unchanged - File does not exist: assets/email_template.txt
files_unchanged - File does not exist: assets/sendmail_template.txt
files_unchanged - File does not exist: assets/nf-core-compile-latex_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-compile-latex_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-compile-latex_logo_dark.png
files_unchanged - File does not exist: docs/README.md
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/compile-latex/compile-latex/.github/workflows/awstest.yml
pipeline_name_conventions - pipeline_name_conventions
template_strings - template_strings
schema_lint - schema_lint
multiqc_config - multiqc_config
modules_config - modules_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
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: 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/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/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: conf/test.config
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: conf/base.config
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-compile-latex_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowCompile-latex.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
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: 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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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 maxulysse/
nextflow_config - Config variable manifest.homePage began with https://github.com/maxulysse/
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.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.publish_dir_mode= move
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 - 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/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 - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 25.10.4, Config: 25.10.4
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting_comment.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: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-04-16 14:08:57

maxulysse added 17 commits September 30, 2022 16:22

replace travisCI by GHA

b001c47

code polish

6f7641d

more polish

778ac31

more polish

586b2ff

convert to DSL2

4bf1fc9

Template update for nf-core/tools version 3.3.1

a9d2c61

strict syntax

5cfcdc4

update container

f48e1ef

add tests

78a9bf7

no HEAD

ffaa471

docker

0cf8326

fix too strict syntax

33f8c1b

keep fail-safe

c219d9c

outdir

ed27027

Merge pull request #15 from maxulysse/strict

c75080c

update README

990dfb4

delete legacy files

e92a299

maxulysse changed the title ~~Release 4.0.0~~ Release 3.0.0 Apr 13, 2026

maxulysse added 12 commits April 14, 2026 10:39

Merge pull request #18 from maxulysse/clean

84c718f

Merge branch 'dev' into template_sync

67c9359

fix lint

6809c9a

Merge branch 'dev' into template_sync

1026b05

Template update for nf-core/tools version 3.5.2

fb53ceb

Merge branch 'TEMPLATE' into template_sync

d5b6585

fix linting

3e8bc34

code polish

758e1ed

add logo

cdd8ec5

Apply suggestion from @maxulysse

14aa7fd

add example

952e62a

fix snapshot

f0fc786

maxulysse added 5 commits April 14, 2026 15:16

Merge pull request #19 from maxulysse/template_sync

87258c2

fix lint

4806c48

Merge pull request #21 from maxulysse/lint

97ed559

Remove conda (#20)

6c5cc9b

simplify docs (#22)

e7ce6ca

maxulysse merged commit c2a65d0 into main Apr 16, 2026
9 of 10 checks passed

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Release 3.0.0#16

Release 3.0.0#16
maxulysse merged 34 commits intomainfrom
dev

maxulysse commented Apr 13, 2026

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github-actions Bot commented Apr 16, 2026 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Apr 13, 2026

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github-actions Bot commented Apr 16, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

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github-actions Bot commented Apr 16, 2026 •

edited

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