Dev -> master for v1.4.0 #205

pinin4fjords · 2023-11-25T00:44:03Z

PR checklist

Post 1.3.1 release changes

Fix sample metadata table in the html report not paginating

…quant test

Co-authored-by: Jonathan Manning <[email protected]>

…into scree

…into mod_updates

Update DESeq2/Limma

…into design

Add design to report

…bundance into transcript_lengths

Transcript lengths for DESeq2

Release v1.4.0

github-actions · 2023-11-25T00:45:37Z

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

Posted for pipeline commit 47ef421

+| ✅ 159 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.4.0

✅ 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/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-differentialabundance_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-differentialabundance_logo_light.png
files_exist - File found: docs/images/nf-core-differentialabundance_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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowDifferentialabundance.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: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
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-differentialabundance_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.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.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 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 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 - 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-differentialabundance_logo_light.png matches the template
files_unchanged - docs/images/nf-core-differentialabundance_logo_light.png matches the template
files_unchanged - docs/images/nf-core-differentialabundance_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/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: 23.10.0, Config: 23.10.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (142 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: release-announcments.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.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 2.10
Run at 2023-11-27 10:26:41

conf/maxquant.config

docs/usage.md

nextflow_schema.json

pinin4fjords · 2023-11-27T10:08:36Z

Thanks for the review @mashehu - fixes in #206

V1.4.0 fixes

pinin4fjords and others added 30 commits October 27, 2023 10:27

Post 1.3.1 release changes

32e135d

[automated] Fix linting with Prettier

ad2e3a2

Merge pull request #186 from nf-core/post_release_v1.3.1

2f65398

Post 1.3.1 release changes

Enabled selecting all genes for exploratory

3c53db4

Add DESeq2 designs to report

1887890

Fixed GSEA section indent in report

aaed90f

Added optional scree plot in report

c68ded1

Added some more explanation text about DE to the report

9fad17b

Added colors to volcano depending on DE status

7c3824a

bumped nextflowversion

795f136

fix Sample metadata table in the html report is not paginating

a66d795

Updated CHANGELOG

0cf6908

Updated CHANGELOG

7bf203c

Update CHANGELOG.md

3cbc989

[automated] Fix linting with Prettier

d679205

Merge pull request #195 from davidecarlson/dev

5abec26

Fix sample metadata table in the html report not paginating

changed remaining instances of NF version

790ab16

changed example NF version back

4cb13bf

Made min version less strict

bbbb8dc

Fixed some more version problems, added exploratory_n_features to max…

4cbbad6

…quant test

Update assets/differentialabundance_report.Rmd

7c7f1de

Co-authored-by: Jonathan Manning <[email protected]>

Update assets/differentialabundance_report.Rmd

8c2b7cc

Co-authored-by: Jonathan Manning <[email protected]>

Update assets/differentialabundance_report.Rmd

370adbe

Co-authored-by: Jonathan Manning <[email protected]>

removed excessive loop for scree plot, set param to default true

9e1f716

update changelog

4747034

Update changelog

7a1b74f

Fix changelog

c929a76

Merge branch 'dev' of https://github.com/nf-core/differentialabundance …

ce7999f

…into scree

Merge branch 'dev' into gsea_indent

ad9d55d

Updated changelog and schema, added gene number to cluster plot titles

ebda620

WackerO and others added 22 commits November 21, 2023 08:20

remove issue from changelog

d13dda1

Merge branch 'dev' of https://github.com/nf-core/differentialabundance …

a722931

…into mod_updates

Update CHANGELOG.md

03857ea

Merge pull request #201 from WackerO/mod_updates

df55a09

Update DESeq2/Limma

Merge branch 'dev' of https://github.com/nf-core/differentialabundance …

1babd7d

…into design

Model is now added to report from the model output files

ea326ae

Made deseq script like the one in dev

b86fbdc

Update changelog

8d5ea35

Merge pull request #189 from WackerO/design

4587680

Add design to report

Update docs

751dc98

Plumb in the new gene length matrices

4299142

[automated] Fix linting with Prettier

330824e

Bump deseq2

e5469e3

Merge branch 'transcript_lengths' of github.com:nf-core/differentiala…

da6f202

…bundance into transcript_lengths

add transcript lengths to test config

1a698cc

[skip ci] update CHANGELOG

8c8bd91

Install deseq from master again

aabb13b

Schema fix

9bf5396

Merge pull request #203 from nf-core/transcript_lengths

0b9aeeb

Transcript lengths for DESeq2

bump versions to 1.4.0

77614e6

Poke CI

4db0bc3

Merge pull request #204 from nf-core/release_v1.4.0

40073de

Release v1.4.0

sateeshperi approved these changes Nov 25, 2023

View reviewed changes

mashehu approved these changes Nov 25, 2023

View reviewed changes

pinin4fjords added 2 commits November 27, 2023 10:02

Address @mashehu feedback for release

56853f5

Poke CI

2341fbd

Merge pull request #206 from nf-core/v1.4.0_fixes

47ef421

V1.4.0 fixes

pinin4fjords merged commit a3d664c into master Nov 27, 2023
29 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Dev -> master for v1.4.0 #205

Dev -> master for v1.4.0 #205

pinin4fjords commented Nov 25, 2023

github-actions bot commented Nov 25, 2023 •

edited

Loading

❗ Test warnings:

✅ Tests passed:

Run details

pinin4fjords commented Nov 27, 2023

Dev -> master for v1.4.0 #205

Dev -> master for v1.4.0 #205

Conversation

pinin4fjords commented Nov 25, 2023

PR checklist

github-actions bot commented Nov 25, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

pinin4fjords commented Nov 27, 2023

github-actions bot commented Nov 25, 2023 •

edited

Loading

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