Don't pass in intervals file to freec by FriederikeHanssen · Pull Request #1214 · nf-core/sarek

FriederikeHanssen · 2023-09-07T12:31:06Z

PR checklist

CHANGELOG.md

FriederikeHanssen · 2023-09-07T12:42:13Z

@nf-core-bot fix linting

…eec_bug

github-actions · 2023-09-07T14:12:14Z

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

Posted for pipeline commit 29eb2d6

+| ✅ 140 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   4 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: .github/workflows/awsfulltest.yml
nextflow_config - Config manifest.version should end in dev: 3.3.0
schema_lint - Input mimetype is missing or empty
schema_description - No description provided in schema for parameter: input_restart

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
actions_ci - actions_ci
template_strings - template_strings
schema_params - schema_params
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: 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-sarek_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-sarek_logo_light.png
files_exist - File found: docs/images/nf-core-sarek_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: .github/workflows/awstest.yml
files_exist - File found: lib/WorkflowSarek.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: 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-sarek_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.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 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 - 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 - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
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_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: branch.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 2.9
Run at 2023-09-07 13:02:06

asp8200 · 2023-09-08T06:49:36Z

LGTM - just waiting for tests to complete.

Don't pass in intervals file to freec

348cef4

FriederikeHanssen requested a review from maxulysse as a code owner September 7, 2023 12:31

FriederikeHanssen commented Sep 7, 2023

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

Update CHANGELOG.md

79c8e16

maxulysse approved these changes Sep 7, 2023

View reviewed changes

FriederikeHanssen added 2 commits September 7, 2023 14:59

Fix caridanlity

4acf210

Merge remote-tracking branch 'origin/controlfreec_bug' into controlfr…

29eb2d6

…eec_bug

Merge branch 'dev' into controlfreec_bug

58457e8

maxulysse merged commit 9085dee into nf-core:dev Sep 8, 2023

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Don't pass in intervals file to freec#1214

Don't pass in intervals file to freec#1214
maxulysse merged 5 commits intonf-core:devfrom
FriederikeHanssen:controlfreec_bug

FriederikeHanssen commented Sep 7, 2023

Uh oh!

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FriederikeHanssen commented Sep 7, 2023

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github-actions bot commented Sep 7, 2023 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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asp8200 commented Sep 8, 2023

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FriederikeHanssen commented Sep 7, 2023

PR checklist

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FriederikeHanssen commented Sep 7, 2023

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github-actions bot commented Sep 7, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

asp8200 commented Sep 8, 2023

Uh oh!

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github-actions bot commented Sep 7, 2023 •

edited

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