Merging template 2.12 #127

JoseEspinosa · 2024-01-30T14:56:08Z

No description provided.

…o merging-template-2.12

github-actions · 2024-01-30T14:57:29Z

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

Posted for pipeline commit d164612

+| ✅ 188 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  11 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: lib/WorkflowProteinfold.groovy
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 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 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 WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
pipeline_todos - TODO string in WorkflowAlphafold2.groovy: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in check_samplesheet.py: Update the script to check the samplesheet
pipeline_todos - TODO string in check_samplesheet.py: Update the check_samplesheet function
pipeline_todos - TODO string in check_samplesheet.py: Update the column names for the input samplesheet

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
multiqc_config - multiqc_config

✅ 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-proteinfold_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-proteinfold_logo_light.png
files_exist - File found: docs/images/nf-core-proteinfold_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: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
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: .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-proteinfold_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 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.mode
nextflow_config - Config default value correct: params.max_template_date
nextflow_config - Config default value correct: params.full_dbs
nextflow_config - Config default value correct: params.alphafold2_mode
nextflow_config - Config default value correct: params.alphafold2_model_preset
nextflow_config - Config default value correct: params.colabfold_server
nextflow_config - Config default value correct: params.colabfold_model_preset
nextflow_config - Config default value correct: params.num_recycle
nextflow_config - Config default value correct: params.use_amber
nextflow_config - Config default value correct: params.db_load_mode
nextflow_config - Config default value correct: params.use_templates
nextflow_config - Config default value correct: params.num_recycles
nextflow_config - Config default value correct: params.custom_config_version
nextflow_config - Config default value correct: params.custom_config_base
nextflow_config - Config default value correct: params.max_cpus
nextflow_config - Config default value correct: params.max_memory
nextflow_config - Config default value correct: params.max_time
nextflow_config - Config default value correct: params.bfd
nextflow_config - Config default value correct: params.small_bfd
nextflow_config - Config default value correct: params.alphafold2_params
nextflow_config - Config default value correct: params.mgnify
nextflow_config - Config default value correct: params.pdb70
nextflow_config - Config default value correct: params.pdb_mmcif
nextflow_config - Config default value correct: params.pdb_obsolete
nextflow_config - Config default value correct: params.uniref30_alphafold2
nextflow_config - Config default value correct: params.uniref90
nextflow_config - Config default value correct: params.pdb_seqres
nextflow_config - Config default value correct: params.uniprot_sprot
nextflow_config - Config default value correct: params.uniprot_trembl
nextflow_config - Config default value correct: params.colabfold_db_link
nextflow_config - Config default value correct: params.uniref30_colabfold_link
nextflow_config - Config default value correct: params.esmfold_3B_v1
nextflow_config - Config default value correct: params.esm2_t36_3B_UR50D
nextflow_config - Config default value correct: params.esm2_t36_3B_UR50D_contact_regression
nextflow_config - Config default value correct: params.publish_dir_mode
nextflow_config - Config default value correct: params.max_multiqc_email_size
nextflow_config - Config default value correct: params.validate_params
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-proteinfold_logo_light.png matches the template
files_unchanged - docs/images/nf-core-proteinfold_logo_light.png matches the template
files_unchanged - docs/images/nf-core-proteinfold_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/NfcoreTemplate.groovy 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 (136 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: release-announcements.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awstest.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
Run at 2024-01-30 22:12:00

mashehu · 2024-01-30T22:10:22Z

@nf-core-bot fix linting

nf-core-bot and others added 4 commits December 19, 2023 19:45

Template update for nf-core/tools version 2.11

28e9b48

Template update for nf-core/tools version 2.11.1

e484f62

Template update for nf-core/tools version 2.12

ccde84d

Merge branch 'TEMPLATE' of https://github.com/nf-core/proteinfold int…

33f224c

…o merging-template-2.12

JoseEspinosa added 3 commits January 30, 2024 17:29

Make prettier happy

940b5b7

Make prettier happy

ba04e5f

Fix schema

104fc22

[automated] Fix linting with Prettier

d164612

mashehu approved these changes Jan 30, 2024

View reviewed changes

JoseEspinosa merged commit 6b27456 into nf-core:dev Jan 30, 2024
6 of 7 checks passed

JoseEspinosa deleted the merging-template-2.12 branch January 30, 2024 22:52

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Merging template 2.12 #127

Merging template 2.12 #127

JoseEspinosa commented Jan 30, 2024

github-actions bot commented Jan 30, 2024 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mashehu commented Jan 30, 2024

Merging template 2.12 #127

Merging template 2.12 #127

Conversation

JoseEspinosa commented Jan 30, 2024

github-actions bot commented Jan 30, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

mashehu commented Jan 30, 2024

github-actions bot commented Jan 30, 2024 •

edited

Loading

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