Batcheffect bugfix by WackerO · Pull Request #130 · qbic-pipelines/rnadeseq

WackerO · 2022-06-15T08:05:22Z

This PR fixes an error that appears when using the batcheffect option.

PR checklist

//TODO: Change nf-core? In "If necessary, also...", this does not make much sense, maybe just delete?

Release 2.0

WackerO · 2022-06-15T08:06:17Z

Does it make sense to add another test config with batch effect enabled? If so, will have to check what needs to be changed in the input data

github-actions · 2022-06-15T08:06:50Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit afad99f

+| ✅ 115 tests passed       |+
#| ❔  29 tests were ignored |#
!| ❗  18 tests had warnings |!
-| ❌   4 tests failed       |-

Details

❌ Test failures:

nextflow_config - Config manifest.name did not begin with nf-core/:
qbic-pipelines/rnadeseq
nextflow_config - Config variable manifest.homePage did not begin with https://github.com/nf-core/:
https://github.com/qbic-pipelines/rnadeseq
multiqc_config - 'assets/multiqc_config.yml' does not meet requirements: Section nf-core-qbic-pipelines/rnadeseq-summary missing in report_section_order
multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.0'
readme - README did not have a Nextflow minimum version badge.
readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
pipeline_todos - TODO string in rnadeseq.nf: Add all file path parameters for the pipeline to the list below
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
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 awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters
schema_description - Ungrouped param in schema: show_hidden_params
schema_description - Ungrouped param in schema: input_type
schema_description - Ungrouped param in schema: genome
schema_description - Ungrouped param in schema: gtf
schema_description - Ungrouped param in schema: organism
schema_description - Ungrouped param in schema: library
schema_description - Ungrouped param in schema: keytype
schema_description - Ungrouped param in schema: igenomes_base
schema_description - Ungrouped param in schema: igenomes_ignore

❔ Tests ignored:

files_exist - File is ignored: assets/nf-core-qbic-pipelines/rnadeseq_logo_light.png
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_light.png
files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_dark.png
files_exist - File is ignored: bin/markdown_to_html.r
files_exist - File is ignored: .github/workflows/push_dockerhub.yml
files_exist - File is ignored: assets/multiqc_config.yaml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
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 does not exist: assets/nf-core-qbic-pipelines/rnadeseq_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_dark.png
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: .gitignore or foo

✅ 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: .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: conf/modules.config
files_exist - File found: conf/test.config
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: 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: 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-qbic-pipelines/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: .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: 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 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 - .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/NfcoreSchema.groovy matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - CI is building the correct docker image: docker build --no-cache . -t qbicpipelines/rnadeseq:dev
actions_ci - CI is pulling the correct docker image: docker pull qbicpipelines/rnadeseq:dev
actions_ci - CI is tagging docker image correctly: docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:dev
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
template_strings - Did not find any Jinja template strings (113 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: awstest.yml
actions_schema_validation - Workflow validation passed: push_dockerhub.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.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' contains 'export_plots: true'.

Run details

nf-core/tools version 2.4.1
Run at 2022-06-22 10:45:03

ggabernet · 2022-06-16T12:50:35Z

yes, it's be great to add a test profile with this batch correction being tested :)

… batch_error

WackerO · 2022-06-21T13:39:25Z

Please do not merge yet even if the tests succeed

WackerO · 2022-06-22T11:18:40Z

Can be merged!

ggabernet

Looks good to me!

ggabernet and others added 2 commits June 2, 2022 11:19

Merge pull request qbic-pipelines#129 from qbic-pipelines/dev

789b138

Release 2.0

Fixed a batch_effect error

294f0ac

WackerO added 4 commits June 21, 2022 12:51

Added test_batcheffect

c95e4e9

Updated config path

44039f8

Merge branch 'dev' of https://github.com/qbic-pipelines/rnadeseq into…

3c18ab2

… batch_error

Corrected changelog

16e7e6b

WackerO added 2 commits June 22, 2022 10:31

Set version to dev

4e6935f

Changed dplyr to 1.0.9

afad99f

ggabernet approved these changes Jun 22, 2022

View reviewed changes

ggabernet merged commit 8e98de2 into qbic-pipelines:dev Jun 22, 2022

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Batcheffect bugfix#130

Batcheffect bugfix#130
ggabernet merged 8 commits intoqbic-pipelines:devfrom
WackerO:batch_error

WackerO commented Jun 15, 2022 •

edited

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WackerO commented Jun 15, 2022

Uh oh!

github-actions Bot commented Jun 15, 2022 •

edited

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❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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ggabernet commented Jun 16, 2022

Uh oh!

WackerO commented Jun 21, 2022

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WackerO commented Jun 22, 2022

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WackerO commented Jun 15, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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PR checklist

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WackerO commented Jun 15, 2022

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github-actions Bot commented Jun 15, 2022 • 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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ggabernet commented Jun 16, 2022

Uh oh!

WackerO commented Jun 21, 2022

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WackerO commented Jun 22, 2022

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WackerO commented Jun 15, 2022 •

edited

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github-actions Bot commented Jun 15, 2022 •

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`nf-core lint` overall result: Failed ❌