Merge template version 3.0.2 #63

itrujnara · 2024-10-14T08:37:35Z

Yet another template merge.

PR checklist

This comment contains a description of changes (with reason).
Make sure your code lints (nf-core lint).

github-actions · 2024-10-14T08:39:10Z

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

Posted for pipeline commit b0f8e7d

+| ✅ 229 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  10 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
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 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 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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ 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-reportho_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-reportho_logo_light.png
files_exist - File found: docs/images/nf-core-reportho_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_ignored.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 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-reportho_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/WorkflowReportho.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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 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 manifest.version ends in dev: 1.1.0dev
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.output_intermediates= false
nextflow_config - Config default value correct: params.use_all= false
nextflow_config - Config default value correct: params.local_databases= false
nextflow_config - Config default value correct: params.offline_run= false
nextflow_config - Config default value correct: params.skip_oma= false
nextflow_config - Config default value correct: params.skip_panther= false
nextflow_config - Config default value correct: params.skip_orthoinspector= false
nextflow_config - Config default value correct: params.orthoinspector_version= Eukaryota2023
nextflow_config - Config default value correct: params.skip_eggnog= false
nextflow_config - Config default value correct: params.use_centroid= false
nextflow_config - Config default value correct: params.min_score= 2.0
nextflow_config - Config default value correct: params.skip_downstream= false
nextflow_config - Config default value correct: params.skip_report= false
nextflow_config - Config default value correct: params.use_structures= false
nextflow_config - Config default value correct: params.iqtree_bootstrap= 1000
nextflow_config - Config default value correct: params.fastme_bootstrap= 100
nextflow_config - Config default value correct: params.skip_orthoplots= false
nextflow_config - Config default value correct: params.skip_iqtree= false
nextflow_config - Config default value correct: params.skip_fastme= false
nextflow_config - Config default value correct: params.skip_treeplots= false
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= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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/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/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-reportho_logo_light.png matches the template
files_unchanged - docs/images/nf-core-reportho_logo_light.png matches the template
files_unchanged - docs/images/nf-core-reportho_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: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 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: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 found and not ignored.
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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - IDENTIFY_SEQ_ONLINE found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_OMA_GROUP_LOCAL found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_PANTHER_GROUP_LOCAL found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_INSPECTOR_GROUP_ONLINE found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_EGGNOG_GROUP_LOCAL found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_CSV found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_SCORE_TABLE found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_HITS found in conf/modules.config and Nextflow scripts.
modules_config - PLOT_ORTHOLOGS found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_HITS_TABLE found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_HITS found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_STATS found in conf/modules.config and Nextflow scripts.
modules_config - MERGE_STATS found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_SEQUENCES_ONLINE found in conf/modules.config and Nextflow scripts.
modules_config - FETCH_AFDB_STRUCTURES found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_TCOFFEETEMPLATE found in conf/modules.config and Nextflow scripts.
modules_config - TCOFFEE_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - IQTREE found in conf/modules.config and Nextflow scripts.
modules_config - PLOT_IQTREE found in conf/modules.config and Nextflow scripts.
modules_config - CONVERT_PHYLIP found in conf/modules.config and Nextflow scripts.
modules_config - FASTME found in conf/modules.config and Nextflow scripts.
modules_config - PLOT_FASTME found in conf/modules.config and Nextflow scripts.
modules_config - DUMP_PARAMS found in conf/modules.config and Nextflow scripts.
modules_config - CONVERT_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - MAKE_REPORT found in conf/modules.config and Nextflow scripts.
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: 3.0.1

Run details

nf-core/tools version 3.0.1
Run at 2024-10-14 08:45:43

.github/CONTRIBUTING.md

CITATIONS.md

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Co-authored-by: Maxime U Garcia <[email protected]>

itrujnara · 2024-10-14T09:19:45Z

Uniprot is currently having issues, will check again in a few hours

itrujnara · 2024-10-14T13:54:01Z

The pull_request_target check seems broken, merging despite it

itrujnara added 3 commits October 14, 2024 10:15

Template update for nf-core/tools version 3.0.1

33d98d2

Merge template version 3.0.2

9ffb7ee

Correct version of changelog

4afc381

Make prettier happy

a9e84e3

mashehu approved these changes Oct 14, 2024

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maxulysse reviewed Oct 14, 2024

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CITATIONS.md Outdated Show resolved Hide resolved

Make prettier happy again

d711525

maxulysse approved these changes Oct 14, 2024

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itrujnara and others added 2 commits October 14, 2024 10:44

Update .github/CONTRIBUTING.md

2d153fe

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update CITATIONS.md

b0f8e7d

Co-authored-by: Maxime U Garcia <[email protected]>

maxulysse approved these changes Oct 14, 2024

View reviewed changes

itrujnara merged commit 43b7529 into nf-core:dev Oct 14, 2024

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Merge template version 3.0.2 #63

Merge template version 3.0.2 #63

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itrujnara commented Oct 14, 2024

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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itrujnara commented Oct 14, 2024

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Merge template version 3.0.2 #63

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itrujnara commented Oct 14, 2024

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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itrujnara commented Oct 14, 2024

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itrujnara commented Oct 14, 2024

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github-actions bot commented Oct 14, 2024 •

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