Add heatmap cluster param, fix enrichment plot labels, use correct plotMA by WackerO · Pull Request #229 · qbic-pipelines/rnadeseq

WackerO · 2024-04-29T12:36:24Z

Add heatmap cluster param, fix enrichment plot labels being cut off, use correct plotMA function as otherwise the plots are empty (the 2.3dev changes are necessary so that the container works).

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

… dev

…heatmaps

github-actions · 2024-04-29T12:37:50Z

`nf-core lint` overall result: Failed ❌

Posted for pipeline commit 920e855

+| ✅ 145 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   8 tests had warnings |!
-| ❌  14 tests failed       |-

Details

❌ Test failures:

files_exist - File must be removed: lib/Utils.groovy
files_exist - File must be removed: lib/WorkflowMain.groovy
files_exist - File must be removed: lib/NfcoreTemplate.groovy
files_exist - File must be removed: lib/WorkflowRnadeseq.groovy
files_exist - File must be removed: lib/nfcore_external_java_deps.jar
nextflow_config - Config default value incorrect: params.software_versions is set as None in nextflow_schema.json but is NO_FILE6 in nextflow.config.
nextflow_config - Config default value incorrect: params.genome is set as None in nextflow_schema.json but is null in nextflow.config.
nextflow_config - Config default value incorrect: params.publish_dir_mode is set as copy in nextflow_schema.json but is null in nextflow.config.
nextflow_config - Config default value incorrect: params.email is set as false in nextflow_schema.json but is null in nextflow.config.
nextflow_config - Config default value incorrect: params.custom_config_base is set as https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version} in nextflow_schema.json but is https://raw.githubusercontent.com/nf-core/configs/master in nextflow.config.
nextflow_config - Config default value incorrect: params.config_profile_description is set as false in nextflow_schema.json but is null in nextflow.config.
nextflow_config - Config default value incorrect: params.config_profile_contact is set as false in nextflow_schema.json but is null in nextflow.config.
nextflow_config - Config default value incorrect: params.config_profile_url is set as false in nextflow_schema.json but is null in nextflow.config.
files_unchanged - .github/workflows/linting_comment.yml does not match the template

❗ Test warnings:

readme - README did not have a Nextflow minimum version badge.
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_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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: assets/multiqc_config.yaml
files_exist - File is ignored: assets/nf-core-qbic-pipelines/rnadeseq_logo_light.png
files_exist - File is ignored: bin/markdown_to_html.r
files_exist - File is ignored: conf/test_full.config
files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_dark.png
files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/rnadeseq_logo_light.png
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: .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: 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/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: 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 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: pipeline_template.yml
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/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-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: 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.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.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 dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: dev
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.input_type= featurecounts
nextflow_config - Config default value correct: params.contrast_matrix= DEFAULT
nextflow_config - Config default value correct: params.contrast_list= DEFAULT1
nextflow_config - Config default value correct: params.contrast_pairs= DEFAULT2
nextflow_config - Config default value correct: params.genelist= NO_FILE
nextflow_config - Config default value correct: params.relevel= NO_FILE2
nextflow_config - Config default value correct: params.logFC_threshold= 0
nextflow_config - Config default value correct: params.adj_pval_threshold= 0.05
nextflow_config - Config default value correct: params.norm_method= rlog
nextflow_config - Config default value correct: params.vst_genes_number= 1000
nextflow_config - Config default value correct: params.round_DE= -1
nextflow_config - Config default value correct: params.set_background= true
nextflow_config - Config default value correct: params.min_DEG_pathway= 1
nextflow_config - Config default value correct: params.heatmaps_cluster_rows= true
nextflow_config - Config default value correct: params.heatmaps_cluster_cols= false
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes
nextflow_config - Config default value correct: params.outdir= ./results
nextflow_config - Config default value correct: params.tracedir= ./results/pipeline_info
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml 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 Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (156 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: push_github_container_reg.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 report_section_order
multiqc_config - 'assets/multiqc_config.yml' contains export_plots
multiqc_config - 'assets/multiqc_config.yml' contains report_comment
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'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.13.1
Run at 2024-04-30 13:17:16

… plot_fixes

d4straub

LGTM, didnt find any potential issue

WackerO added 8 commits October 10, 2023 16:15

Changed versions to dev

6ca2eab

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

63cc932

… dev

moved heatmap_genelist output to differential analysis results folder

33f01b9

removed ensembl_id col from pathway heatmaps

582e71f

fixed plotma issue with empty plots, added clutser param for pathway …

ebbcf04

…heatmaps

working on removing irrelevant samples from heatmaps_norm

0789481

Undid some changes about sample filtering for heatmaps

b01328b

Fixed enrichment plots having their y labels cut off

ce9bf0a

WackerO and others added 7 commits April 29, 2024 14:41

Update changelog

dab8978

updated test profiles

cb0c1e4

fixed heatmap test path

fb9a4bd

fixed test profile

f1edb41

Merge branch 'dev' into plot_fixes

4f64abd

fixed md5sum

e3a8f66

Merge branch 'plot_fixes' of https://github.com/WackerO/rnadeseq into…

920e855

… plot_fixes

d4straub approved these changes May 2, 2024

View reviewed changes

WackerO merged commit f7c1ccc into qbic-pipelines:dev May 2, 2024

WackerO deleted the plot_fixes branch May 2, 2024 11:15

This was referenced May 3, 2024

Order the pathway heatmaps according to condition #224

Closed

Double-colored bar in enrichment plot, some slashes missing #185

Closed

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Add heatmap cluster param, fix enrichment plot labels, use correct plotMA#229

Add heatmap cluster param, fix enrichment plot labels, use correct plotMA#229
WackerO merged 15 commits intoqbic-pipelines:devfrom
WackerO:plot_fixes

WackerO commented Apr 29, 2024

Uh oh!

github-actions Bot commented Apr 29, 2024 •

edited

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❔ Tests ignored:

✅ Tests passed:

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WackerO commented Apr 29, 2024

PR checklist

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github-actions Bot commented Apr 29, 2024 • 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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github-actions Bot commented Apr 29, 2024 •

edited

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`nf-core lint` overall result: Failed ❌