separate ascat and controlfreec ploidy by FriederikeHanssen · Pull Request #663 · nf-core/sarek

FriederikeHanssen · 2022-07-19T20:58:38Z

ASCAT ploidy and ControlFREEC ploidy parameters are both specified completely differently. If only one parameter caters to both tools, you could not run both tools in parallel very well.

github-actions · 2022-07-19T21:00:17Z

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

Posted for pipeline commit c5ab1a1

+| ✅ 146 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

Details

❗ Test warnings:

readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

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

✅ Tests passed:

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nextflow_config - Config variable found: manifest.name
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nextflow_config - Config variable (correctly) not found: params.version
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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 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: '3.0dev'
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
files_unchanged - .gitattributes matches the template
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files_unchanged - lib/nfcore_external_java_deps.jar matches the template
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files_unchanged - .gitignore 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 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 (384 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: local_modules.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest_somatic.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.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 2.4.1
Run at 2022-07-19 20:59:54

SusiJo · 2022-07-20T05:49:25Z

Thanks for changing the ploidy, makes sense to separate them 👍

separate ascat and controlfreec ploidy

c5ab1a1

FriederikeHanssen requested a review from maxulysse as a code owner July 19, 2022 20:58

add params to schema

ea17f5d

maxulysse approved these changes Jul 20, 2022

View reviewed changes

maxulysse merged commit e5a4ffb into nf-core:dev Jul 20, 2022

FriederikeHanssen deleted the ascat_controlfreec_ploidy branch July 10, 2023 19:00

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separate ascat and controlfreec ploidy#663

separate ascat and controlfreec ploidy#663
maxulysse merged 2 commits intonf-core:devfrom
FriederikeHanssen:ascat_controlfreec_ploidy

FriederikeHanssen commented Jul 19, 2022

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github-actions bot commented Jul 19, 2022 •

edited

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SusiJo commented Jul 20, 2022

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FriederikeHanssen commented Jul 19, 2022

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nf-core lint overall result: Passed ✅ ⚠️

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SusiJo commented Jul 20, 2022

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github-actions bot commented Jul 19, 2022 •

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