Release 2.2 by WackerO · Pull Request #219 · qbic-pipelines/rnadeseq

WackerO · 2023-08-18T07:32:40Z

PR checklist

… dev

lists the file names --> also added to the pytests

1) Fix enriched pathways display error in report

2) Add optional --quote param

3) Add gprofiler version

4) No alignfiles

… heatmap_sizes

1) Scaling heatmap sizes

… optional_versions

…n faster on github now

…ronment change

Added boxplots after batcheffect; boxplots now from transformed data; boxplot titles and filenames now also with genename; increased threshold before overlapping PCA labels are hidden

… missingnames

Replace missing GTF gene_names with IDs

Software version bumps for release 2.2

github-actions · 2023-08-18T07:38:40Z

This PR is against the `master` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

Hi @WackerO,

It looks like this pull-request is has been made against the qbic-pipelines/rnadeseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the qbic-pipelines/rnadeseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions · 2023-08-18T07:44:56Z

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

Posted for pipeline commit c30e7eb

+| ✅ 125 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   9 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.2
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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
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 awsfulltest.yml: You can customise AWS full pipeline tests as required
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: 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: lib/nfcore_external_java_deps.jar
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 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: .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 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/NfcoreTemplate.groovy 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 (154 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: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: push_github_container_reg.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: branch.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'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.9
Run at 2023-08-21 06:55:37

jonasscheid

LGTM from a more outside perspective. Maybe add authors and licence to the core script of the pipeline

jonasscheid · 2023-08-18T10:10:50Z

Maybe add authors and MIT licence here

louperelo

Looks good to me.
Just found some minor typos and had a question regarding boolean parameters.

Co-authored-by: Louisa Perelo <44900284+louperelo@users.noreply.github.com>

Add suggestions for release 2.2

WackerO · 2023-08-21T08:40:57Z

Will merge this against branch protections as Jonas has also approved, just without write access. Thanks for the reviews, Louisa and Jonas!

WackerO and others added 30 commits February 7, 2023 09:38

Fixed ##Enriched Pathways problem in report

e8c6120

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

4c89294

… dev

Updated changelog

f0829f5

prettier

db1732c

Added optional --quote

83bffa3

changed container to dev

e8a2a2f

Added gprofiler version string to report

da4e786

rm trailing whitespace

3bfbe17

added some missing SVG calls

b2092a3

Changed text for quote/offer in report

01f4bda

Updated 5sum for rsem

b37a605

removed rsem/salmon files from output.zip, instead added txt file which

babba2e

lists the file names --> also added to the pytests

Updated documentation (also in report)

7d3f402

Fixed rsem test

c7f7c29

Merge pull request #195 from WackerO/dev

7e49936

1) Fix enriched pathways display error in report

Merge pull request #196 from WackerO/quote

ac8e593

2) Add optional --quote param

Merge pull request #197 from WackerO/gprofiler

189cc7d

3) Add gprofiler version

Merge pull request #198 from WackerO/no_alignfiles

52bb677

4) No alignfiles

Heatmap sizes scale depending on data

ea3ce9b

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

950a8d3

… heatmap_sizes

bugfix

bbaa605

Made software_versions optional

7c4a4a1

Updated docs

cc3b89d

Merge pull request #199 from WackerO/heatmap_sizes

4c7f77e

1) Scaling heatmap sizes

Renamed variable

ac55c9d

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

27ede77

… optional_versions

Updated some 5sums, set a logFC for test_full in the hopes it will ru…

fbfadb6

…n faster on github now

updated 5sums for test_full after adding logfc

66a6125

Updated md5sums

2ea47a4

commented out two md5sums as they constantly change even without envi…

4562671

…ronment change

WackerO and others added 12 commits August 16, 2023 14:47

replaced missing gene_names in gtf with gene_ids

823169f

Boxplots now also have their gene names in title and filename

0b7a721

Corrected changelog

d1a01df

fixed missing labels in PCA_label plots

cbf3915

updated changelog

4957b14

Merge pull request #215 from WackerO/boxplots

ff84b38

Added boxplots after batcheffect; boxplots now from transformed data; boxplot titles and filenames now also with genename; increased threshold before overlapping PCA labels are hidden

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

2089e26

… missingnames

Merge pull request #217 from WackerO/missingnames

895c630

Replace missing GTF gene_names with IDs

Software version bumps for release

3f4ac36

modified some comments

92db42d

Fixed changelog

cf4487f

Merge pull request #218 from WackerO/release_2_2

7b5c9bd

Software version bumps for release 2.2

jonasscheid reviewed Aug 18, 2023

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jonasscheid Aug 18, 2023

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Maybe add authors and MIT licence here

WackerO reacted with thumbs up emoji

jonasscheid approved these changes Aug 18, 2023

View reviewed changes

louperelo approved these changes Aug 18, 2023

View reviewed changes

WackerO and others added 6 commits August 18, 2023 15:52

Update nextflow_schema.json

0f63439

Co-authored-by: Louisa Perelo <44900284+louperelo@users.noreply.github.com>

Update nextflow_schema.json

a83a94b

Co-authored-by: Louisa Perelo <44900284+louperelo@users.noreply.github.com>

Update nextflow_schema.json

ccb67df

Co-authored-by: Louisa Perelo <44900284+louperelo@users.noreply.github.com>

Update docs/usage.md

28d8763

Co-authored-by: Louisa Perelo <44900284+louperelo@users.noreply.github.com>

Update docs/usage.md

1860521

Co-authored-by: Louisa Perelo <44900284+louperelo@users.noreply.github.com>

smaller clean-up changes

4739c0a

WackerO changed the title ~~Release 2.2~~ Release 2.2 fixes Aug 21, 2023

WackerO changed the title ~~Release 2.2 fixes~~ Release 2.2 Aug 21, 2023

WackerO and others added 3 commits August 21, 2023 08:27

Added some suggestions from review by louperelo and jonasscheid

48f4a47

modified changelog

7c33a84

Merge pull request #220 from WackerO/release_2_2

c30e7eb

Add suggestions for release 2.2

WackerO merged commit f5e54b6 into master Aug 21, 2023

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Release 2.2#219
WackerO merged 158 commits intomasterfrom
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WackerO commented Aug 18, 2023

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edited

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✅ Tests passed:

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WackerO commented Aug 21, 2023

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WackerO commented Aug 18, 2023

PR checklist

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This PR is against the master branch ❌

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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WackerO commented Aug 21, 2023

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github-actions Bot commented Aug 18, 2023 •

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