Sync 3 #29

erikrikarddaniel · 2025-01-16T18:25:08Z

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/phyloplace branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

Template update plus some documentation things.

The linting warning can't be fixed as the pipeline doesn't have an --input param, but two different params.

…o sync-3.0

github-actions · 2025-01-16T18:26:23Z

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

Posted for pipeline commit 1f904ba

+| ✅ 202 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

schema_lint - Parameter input not found in schema

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config
nextflow_config - Config variable ignored: params.input

✅ 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-phyloplace_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-phyloplace_logo_light.png
files_exist - File found: docs/images/nf-core-phyloplace_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 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-phyloplace_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/WorkflowPhyloplace.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: 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.id= placement
nextflow_config - Config default value correct: params.alignmethod= hmmer
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/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/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-phyloplace_logo_light.png matches the template
files_unchanged - docs/images/nf-core-phyloplace_logo_light.png matches the template
files_unchanged - docs/images/nf-core-phyloplace_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.
pipeline_todos - No TODO strings found
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_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: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: ci.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 - HMMER_HMMSEARCH found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_HMMBUILD found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_UNALIGNREF found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_HMMALIGNREF found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_HMMALIGNQUERY found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_MASK found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_MASKQUERY found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_MASKREF found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_AFAFORMATQUERY found in conf/modules.config and Nextflow scripts.
modules_config - HMMER_AFAFORMATREF found in conf/modules.config and Nextflow scripts.
modules_config - MAFFT found in conf/modules.config and Nextflow scripts.
modules_config - EPANG_PLACE found in conf/modules.config and Nextflow scripts.
modules_config - GAPPA_GRAFT found in conf/modules.config and Nextflow scripts.
modules_config - GAPPA_ASSIGN found in conf/modules.config and Nextflow scripts.
modules_config - GAPPA_HEATTREE found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC 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: 3.1.1

Run details

nf-core/tools version 3.1.1
Run at 2025-01-17 14:22:14

d4straub

Looks good te me, couldnt find any problem!
Probably it would be time for a release after all that template updates?

d4straub · 2025-01-17T07:37:32Z

ro-crate-metadata.json

+        {
+            "@id": "#[email protected]",
+            "@type": "Person",
+            "email": "[email protected]",


Thats a different email than the one in nextflow.config.
But that file is new and I dont really now whats supposed to be here.

Hawkeyed! Thanks! :-)

erikrikarddaniel added 20 commits December 18, 2024 18:37

Template update for nf-core/tools version 3.0.2

34a48e0

nf-core 3.0.2 merge, cli tests pass

faebec5

Add config and update software version file name to make nf-tests pass

6676cc5

Lint update module keys

1da97e5

Remove params.genomes warnings

584c7aa

Delete obsolete mafft module files

d95c178

Update modules

95a77b7

Fix linting errors

3cdb60c

Removed mafft from modules.json

7f4a548

Template update for nf-core/tools version 3.1.1

53f1d53

3.1.1 merge

d12a519

get paramsSummaryMap back

92d0e40

Yet another software version file name

f43ad4c

Fix linting issues

d218e26

Update README.md

540945e

Add citation for clustalo

dec7129

Merge branch 'sync-3.0' of github.com:erikrikarddaniel/phyloplace int…

3679806

…o sync-3.0

Template update for nf-core/tools version 3.1.1

cb40f22

Merge branch 'TEMPLATE' into sync-3.0

a9ab6aa

Update ro-create-metadata.json

7faf480

erikrikarddaniel requested a review from d4straub January 16, 2025 18:38

Update CHANGELOG.md

0d93dea

d4straub approved these changes Jan 17, 2025

View reviewed changes

Update emails and id

1f904ba

erikrikarddaniel merged commit f5314ad into nf-core:dev Jan 17, 2025
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Sync 3 #29

Sync 3 #29

erikrikarddaniel commented Jan 16, 2025 •

edited

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github-actions bot commented Jan 16, 2025 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

d4straub left a comment •

edited

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d4straub Jan 17, 2025

erikrikarddaniel Jan 17, 2025

Sync 3 #29

Sync 3 #29

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erikrikarddaniel commented Jan 16, 2025 • edited Loading

PR checklist

github-actions bot commented Jan 16, 2025 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

d4straub left a comment • edited Loading

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d4straub Jan 17, 2025

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erikrikarddaniel Jan 17, 2025

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erikrikarddaniel commented Jan 16, 2025 •

edited

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github-actions bot commented Jan 16, 2025 •

edited

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

d4straub left a comment •

edited

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