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Important! Template update for nf-core/tools v2.5
Version 2.5
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-2.5
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/developers/sync.
For more information about this release of nf-core/tools, please see the v2.5
release page.
Python linting (black
) is failing
To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:
- Install
black
:pip install black
- Fix formatting errors in your pipeline:
black .
Once you push these changes the test should pass, and you can hide this comment :+1:
We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
Thanks again for your contribution!
Python linting (black
) is failing
To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:
- Install
black
:pip install black
- Fix formatting errors in your pipeline:
black .
Once you push these changes the test should pass, and you can hide this comment :+1:
We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
Thanks again for your contribution!
nf-core lint
overall result: Passed :white_check_mark:
Posted for pipeline commit 5a86a04
+| ✅ 152 tests passed |+
:white_check_mark: 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:
CODE_OF_CONDUCT.md
-
files_exist - File found:
LICENSE
orLICENSE.md
orLICENCE
orLICENCE.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
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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-rnafusion_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-rnafusion_logo_light.png
-
files_exist - File found:
docs/images/nf-core-rnafusion_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/nfcore_external_java_deps.jar
-
files_exist - File found:
lib/NfcoreSchema.groovy
-
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/WorkflowRnafusion.groovy
-
files_exist - File found:
modules.json
-
files_exist - File not found check:
Singularity
-
files_exist - File not found check:
parameters.settings.json
-
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-rnafusion_logo.png
-
files_exist - File not found check:
.markdownlint.yml
-
files_exist - File not found check:
.yamllint.yml
-
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.show_hidden_params
-
nextflow_config - Config variable found:
params.schema_ignore_params
-
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.version
-
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
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 withnf-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 indev
:'2.2.0dev'
-
nextflow_config - Config
params.custom_config_version
is set tomaster
-
nextflow_config - Config
params.custom_config_base
is set tohttps://raw.githubusercontent.com/nf-core/configs/master
- nextflow_config - Lines for loading custom profiles found
-
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-rnafusion_logo_light.png
matches the template -
files_unchanged -
docs/images/nf-core-rnafusion_logo_light.png
matches the template -
files_unchanged -
docs/images/nf-core-rnafusion_logo_dark.png
matches the template -
files_unchanged -
docs/README.md
matches the template -
files_unchanged -
lib/nfcore_external_java_deps.jar
matches the template -
files_unchanged -
lib/NfcoreSchema.groovy
matches the template -
files_unchanged -
lib/NfcoreTemplate.groovy
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:
21.10.3
, Config:21.10.3
-
readme - README Nextflow minimum version in Quick Start section matched config. README:
21.10.3
, Config:21.10.3
- pipeline_todos - No TODO strings found
- pipeline_name_conventions - Name adheres to nf-core convention
- template_strings - Did not find any Jinja template strings (172 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
- actions_schema_validation - Workflow validation passed: linting.yml
- actions_schema_validation - Workflow validation passed: awsfulltest.yml
- actions_schema_validation - Workflow validation passed: fix-linting.yml
- actions_schema_validation - Workflow validation passed: branch.yml
- actions_schema_validation - Workflow validation passed: awstest.yml
- actions_schema_validation - Workflow validation passed: linting_comment.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' 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'.
Run details
- nf-core/tools version 2.5
- Run at
2022-08-31 08:59:00
Version 2.5.1
of the nf-core/tools pipeline template has just been released. This pull-request is now outdated and has been closed in favour of https://github.com/nf-core/rnafusion/pull/275
Please use https://github.com/nf-core/rnafusion/pull/275 to merge in the new changes from the nf-core template as soon as possible.