Add tests #80

skrakau · 2023-06-23T15:01:51Z

Added a mean comparison to the entity binding ratio boxplots.
Added a param hide_pvalue to not show p-value in plots
Improved handling of command line arguments for R script

PR checklist

github-actions · 2023-06-23T15:03:28Z

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

Posted for pipeline commit d16d3aa

+| ✅ 157 tests passed       |+
!| ❗  12 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
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 output.md: Write this documentation describing your workflow's output
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
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

✅ Tests passed:

files_exist - File found: .gitattributes
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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
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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
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files_exist - File found: assets/email_template.html
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files_exist - File found: conf/modules.config
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files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-metapep_logo_light.png
files_exist - File found: docs/images/nf-core-metapep_logo_dark.png
files_exist - File found: docs/output.md
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files_exist - File found: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreSchema.groovy
files_exist - File found: lib/NfcoreTemplate.groovy
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files_exist - File found: lib/WorkflowMain.groovy
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files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowMetapep.groovy
files_exist - File found: modules.json
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files_exist - File not found check: Singularity
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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-metapep_logo.png
files_exist - File not found check: .markdownlint.yml
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files_exist - File not found check: lib/Checks.groovy
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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.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.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 manifest.version ends in dev: '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
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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 - assets/nf-core-metapep_logo_light.png matches the template
files_unchanged - docs/images/nf-core-metapep_logo_light.png matches the template
files_unchanged - docs/images/nf-core-metapep_logo_dark.png matches the template
files_unchanged - docs/README.md 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
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml 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 badge matched config. Badge: 22.10.1, Config: 22.10.1
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (130 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.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: 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 a matching 'report_comment'.
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 2.8
Run at 2023-06-28 11:21:54

Move some operations to subworkflow

Typo and documentation suggestions Co-authored-by: Sabrina Krakau <[email protected]>

Co-authored-by: Sabrina Krakau <[email protected]>

skrakau · 2023-06-27T12:52:45Z

Waiting for BioContainers/multi-package-containers#2659 to allow final test

Fix params

tillenglert

Some minor comments but LGTM!

modules/local/plot_entity_binding_ratios.nf

nextflow_schema.json

bin/plot_entity_binding_ratios.R

Co-authored-by: Till E. <[email protected]>

tillenglert and others added 20 commits June 27, 2023 14:47

Clean up modules.config

5e62a1b

hide binder thresholds

16a939a

Renaming input check and samplesheet check;

fafa60d

Move some operations to subworkflow

change module name in modules.config

4df778b

Adjust output docs to match process/subworkflow name again

c27dd8b

Update chanelog

5c59d21

Rename script from input_to_datamodel module

87c569c

[automated] Fix linting with Prettier

ae0b640

Standardise commenting in main workflow

aecbe37

Apply suggestions from code review

eb724e1

Typo and documentation suggestions Co-authored-by: Sabrina Krakau <[email protected]>

Changed documentation and function name

fbf8233

rename subworkflow and check samplesheet module

824a295

Update Epytope version to 3.3.1

90db8b8

Reduce peptide length in test_mouse

f7172f0

Update Changelog

6a759dc

[automated] Fix linting with Prettier

75abe53

Update conf/test_mouse.config

0e519b5

Co-authored-by: Sabrina Krakau <[email protected]>

Shorten documentation in test_mouse

823a8e9

Add statistical test to binding ratio boxplots

46c6d07

Improve R command line args handling and add param show_pvalue

3f48477

skrakau force-pushed the add_tests branch from cd1d256 to 3f48477 Compare June 27, 2023 12:51

skrakau added 2 commits June 27, 2023 15:21

Update container

4603399

Merge 'dev' into add_tests

1258b11

skrakau marked this pull request as ready for review June 28, 2023 10:01

skrakau requested a review from tillenglert June 28, 2023 10:02

skrakau added 2 commits June 28, 2023 12:16

Change show_pvalue param to hide_pvalue

a1fc576

Fix params

Update CHANGELOG

279ca11

skrakau force-pushed the add_tests branch from 36bc17e to 279ca11 Compare June 28, 2023 10:18

tillenglert approved these changes Jun 28, 2023

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modules/local/plot_entity_binding_ratios.nf Outdated Show resolved Hide resolved

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nextflow_schema.json Outdated Show resolved Hide resolved

bin/plot_entity_binding_ratios.R Outdated Show resolved Hide resolved

skrakau and others added 2 commits June 28, 2023 13:15

Apply suggestions from code review

408dd7b

Co-authored-by: Till E. <[email protected]>

Fix whitespace

d16d3aa

skrakau merged commit 0dc3b19 into nf-core:dev Jun 28, 2023
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Add tests #80

Add tests #80

skrakau commented Jun 23, 2023 •

edited

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github-actions bot commented Jun 23, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

skrakau commented Jun 27, 2023

tillenglert left a comment

Add tests #80

Add tests #80

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skrakau commented Jun 23, 2023 • edited Loading

PR checklist

github-actions bot commented Jun 23, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

skrakau commented Jun 27, 2023

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skrakau commented Jun 23, 2023 •

edited

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github-actions bot commented Jun 23, 2023 •

edited

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