Fixed batch correction for star input (2.5) by WackerO · Pull Request #159 · qbic-pipelines/rnadeseq

WackerO · 2022-09-01T12:32:12Z

This PR enables batch correction for rsem/salmon input which previously did not work and improves the error messages if some rsem/salmon files are not found. Closes #155

PR checklist

github-actions · 2022-09-01T12:34:16Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit 20a48e3

+| ✅ 119 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   9 tests had warnings |!
-| ❌   4 tests failed       |-

Details

❌ Test failures:

files_exist - File not found: .prettierignore
files_unchanged - lib/NfcoreTemplate.groovy does not match the template
actions_ci - '.github/workflows/ci.yml' does not check minimum NF version
multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

files_exist - File not found: pyproject.toml
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 awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
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.
schema_lint - Parameter input not found in schema

❔ 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 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: .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-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/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: lib/WorkflowRnadeseq.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: 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: .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 manifest.version ends in dev: '2.1.0dev'
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
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/NfcoreSchema.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_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
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (120 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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: push_dockerhub.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 'export_plots: true'.

Run details

nf-core/tools version 2.5.1
Run at 2022-09-05 08:58:53

ggabernet

Looks good to me, just a couple of minor comments

Fixed batch correction for star input

29a9c62

WackerO requested a review from SusiJo September 1, 2022 12:32

WackerO marked this pull request as ready for review September 1, 2022 12:32

WackerO mentioned this pull request Sep 1, 2022

Docu of how to use batch effect is misleading #155

Closed

WackerO added 4 commits September 1, 2022 14:44

Updated Changelog

70a27e8

Changed some error messages

384d021

Changed error messages for rsem/salmon files to be more helpful

83f00a0

Fixed print_string, fixed indentations

20a48e3

WackerO requested a review from ggabernet September 5, 2022 08:57

ggabernet approved these changes Sep 5, 2022

View reviewed changes

Comment thread assets/RNAseq_report.Rmd Outdated

Comment thread assets/RNAseq_report.Rmd Outdated

Fixed typo

3b48804

WackerO merged commit 7588af3 into qbic-pipelines:dev Sep 5, 2022

WackerO deleted the batch branch September 5, 2022 12:06

WackerO mentioned this pull request Sep 22, 2022

Improve error message salmon input #154

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Fixed batch correction for star input (2.5)#159

Fixed batch correction for star input (2.5)#159
WackerO merged 6 commits intoqbic-pipelines:devfrom
WackerO:batch

WackerO commented Sep 1, 2022 •

edited

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github-actions Bot commented Sep 1, 2022 •

edited

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❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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WackerO commented Sep 1, 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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github-actions Bot commented Sep 1, 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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WackerO commented Sep 1, 2022 •

edited

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github-actions Bot commented Sep 1, 2022 •

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`nf-core lint` overall result: Failed ❌