fixed relevel bug by WackerO · Pull Request #208 · qbic-pipelines/rnadeseq

WackerO · 2023-07-03T06:46:53Z

This PR finally (!) makes relevel functional

PR checklist

github-actions · 2023-07-03T06:48:29Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit 1bc3887

+| ✅ 120 tests passed       |+
#| ❔  27 tests were ignored |#
!| ❗  10 tests had warnings |!
-| ❌   3 tests failed       |-

Details

❌ Test failures:

nextflow_config - Config variable not found: params.validationShowHiddenParams
nextflow_config - Config variable not found: params.validationSchemaIgnoreParams
schema_params - Param schema_ignore_params from nextflow config not found in nextflow_schema.json

❗ Test warnings:

readme - README did not have a Nextflow minimum version badge.
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in rnadeseq.nf: Add all file path parameters for the pipeline to the list below
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 prefered methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
schema_lint - Parameter input is not defined in the correct subschema (input_output_options)
system_exit - System.exit in WorkflowMain.groovy: System.exit(1) [line 85]
system_exit - System.exit in WorkflowRnadeseq.groovy: System.exit(1) [line 67]

❔ Tests ignored:

files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/push_dockerhub.yml
files_exist - File is ignored: assets/multiqc_config.yaml
files_exist - File is ignored: assets/nf-core-qbic-pipelines/rnadeseq_logo_light.png
files_exist - File is ignored: bin/markdown_to_html.r
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_dark.png
files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_light.png
files_exist - File is ignored: lib/WorkflowQbic-pipelines/rnadeseq.groovy
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nextflow_config - Config variable ignored: params.input
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ 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 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/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-rnadeseq_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: docs/images/nf-core-rnadeseq_logo_light.png
files_exist - File found: docs/images/nf-core-rnadeseq_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/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: lib/WorkflowRnadeseq.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: .nf-core.yaml
files_exist - File not found check: conf/aws.config
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-rnadeseq_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: .travis.yml
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: 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: 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 dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 2.2dev
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
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - lib/nfcore_external_java_deps.jar 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 Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (132 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
actions_schema_validation - Workflow validation passed: push_github_container_reg.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.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' follows the ordering scheme of the minimally required plugins.
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 2.9
Run at 2023-07-11 12:39:05

SusiJo

LGTM :)

SusiJo · 2023-07-11T13:06:09Z

At some point you should tackle some of the linting problems.

WackerO · 2023-07-11T13:16:01Z

Of course, I'll deal with that in the template update :)
Thanks for reviewing!

fixed releve bug, changelog is already updated

339f672

WackerO added 3 commits July 3, 2023 08:53

nf-core lint

691bcc4

updated test.yml

1229e8b

changed md5sum

f59f142

SusiJo reviewed Jul 11, 2023

View reviewed changes

Comment thread assets/RNAseq_report.Rmd

SusiJo reviewed Jul 11, 2023

View reviewed changes

Comment thread tests/test_relevel.yml

SusiJo reviewed Jul 11, 2023

View reviewed changes

Comment thread tests/test_relevel.yml Outdated

SusiJo reviewed Jul 11, 2023

View reviewed changes

Comment thread assets/RNAseq_report.Rmd

Changed filenames of histograms of p values

1bc3887

SusiJo approved these changes Jul 11, 2023

View reviewed changes

WackerO merged commit a8a2265 into qbic-pipelines:dev Jul 11, 2023

WackerO deleted the relevel branch July 11, 2023 13:16

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fixed relevel bug#208

fixed relevel bug#208
WackerO merged 5 commits intoqbic-pipelines:devfrom
WackerO:relevel

WackerO commented Jul 3, 2023 •

edited

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github-actions Bot commented Jul 3, 2023 •

edited

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❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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SusiJo commented Jul 11, 2023

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WackerO commented Jul 11, 2023

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WackerO commented Jul 3, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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PR checklist

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github-actions Bot commented Jul 3, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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SusiJo left a comment

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SusiJo commented Jul 11, 2023

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WackerO commented Jul 11, 2023

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WackerO commented Jul 3, 2023 •

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github-actions Bot commented Jul 3, 2023 •

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`nf-core lint` overall result: Failed ❌