Important! Template update for nf-core/tools v2.12 #120

nf-core-bot · 2024-01-29T15:54:16Z

Version 2.12 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.12 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v2.12 release page.

github-actions · 2024-02-01T16:01:38Z

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

Posted for pipeline commit ca46c28

+| ✅ 188 tests passed       |+
!| ❗   4 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
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 WorkflowRnavar.groovy: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ 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-rnavar_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-rnavar_logo_light.png
files_exist - File found: docs/images/nf-core-rnavar_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: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowRnavar.groovy
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-rnavar_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.read_length= 150.0
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.aligner= star
nextflow_config - Config default value correct: params.star_max_memory_bamsort= 0
nextflow_config - Config default value correct: params.star_bins_bamsort= 50
nextflow_config - Config default value correct: params.star_max_collapsed_junc= 1000000
nextflow_config - Config default value correct: params.seq_platform= illumina
nextflow_config - Config default value correct: params.gatk_hc_call_conf= 20.0
nextflow_config - Config default value correct: params.vep_cache= s3://annotation-cache/vep_cache/
nextflow_config - Config default value correct: params.snpeff_cache= s3://annotation-cache/snpeff_cache/
nextflow_config - Config default value correct: params.dbnsfp_fields= rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF
nextflow_config - Config default value correct: params.vep_custom_args= --everything --filter_common --per_gene --total_length --offline --format vcf
nextflow_config - Config default value correct: params.vep_out_format= vcf
nextflow_config - Config default value correct: params.gatk_interval_scatter_count= 25
nextflow_config - Config default value correct: params.gatk_vf_window_size= 35
nextflow_config - Config default value correct: params.gatk_vf_cluster_size= 3
nextflow_config - Config default value correct: params.gatk_vf_fs_filter= 30.0
nextflow_config - Config default value correct: params.gatk_vf_qd_filter= 2.0
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 - .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-rnavar_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnavar_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnavar_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml 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 (309 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
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 2.12.1
Run at 2024-02-01 16:39:05

jfy133

Missing changelog update but otherwise LGTM

jfy133 · 2024-02-02T08:06:34Z

nextflow_schema.json

                "read_length": {
                    "type": "number",
-                    "default": 151,
+                    "default": 150,


CHANGELOG update?

maxulysse · 2024-02-02T08:17:59Z

Missing changelog update but otherwise LGTM

I'll take care of that in separate PR, I have other missing entries

nf-core-bot and others added 4 commits January 29, 2024 15:13

Template update for nf-core/tools version 2.12

1f25a71

Merge branch 'dev' into nf-core-template-merge-2.12

18726fe

fix schema

ce95d67

template logo

c226ebe

maxulysse added 4 commits February 1, 2024 17:02

update .editorconfig

06d30fe

prettier

ccce756

editor config

9f45743

logo from template

ca46c28

maxulysse approved these changes Feb 1, 2024

View reviewed changes

jfy133 approved these changes Feb 2, 2024

View reviewed changes

nextflow_schema.json

"read_length": {

"type": "number",

"default": 151,

"default": 150,

Copy link

Member

jfy133 Feb 2, 2024

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

CHANGELOG update?

maxulysse merged commit ebb949b into dev Feb 2, 2024

maxulysse deleted the nf-core-template-merge-2.12 branch February 12, 2024 14:53

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Important! Template update for nf-core/tools v2.12 #120

Important! Template update for nf-core/tools v2.12 #120

Uh oh!

nf-core-bot commented Jan 29, 2024

Uh oh!

github-actions bot commented Feb 1, 2024 •

edited

Loading

❗ Test warnings:

✅ Tests passed:

Run details

Uh oh!

jfy133 left a comment

Uh oh!

jfy133 Feb 2, 2024

Uh oh!

maxulysse commented Feb 2, 2024

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Important! Template update for nf-core/tools v2.12 #120

Important! Template update for nf-core/tools v2.12 #120

Uh oh!

Conversation

nf-core-bot commented Jan 29, 2024

Uh oh!

github-actions bot commented Feb 1, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

Uh oh!

jfy133 left a comment

Choose a reason for hiding this comment

Uh oh!

jfy133 Feb 2, 2024

Choose a reason for hiding this comment

Uh oh!

maxulysse commented Feb 2, 2024

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

github-actions bot commented Feb 1, 2024 •

edited

Loading

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