Dev -> master for v1.3.0 #178

pinin4fjords · 2023-10-19T15:08:27Z

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- [ ] If necessary, also make a PR on the nf-core/differentialabundance branch on the nf-core/test-datasets repository.
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).

Co-authored-by: Jasmin Frangenberg <[email protected]>

Template update for nf-core/tools v2.8

Add spaces to satisfy nf-core download for singularity

Posible fix for issue #127

Module updates to fit with recent registry changes

…ance into diff_docs

document reasons for lack of differential expression

Deseq2 tip

Fix metro map

Don't use contrasts directly from the input channel

Bump shinyngs

Release v1.3.0

github-actions · 2023-10-19T15:10:11Z

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

Posted for pipeline commit 0d4b452

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

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.3.0

✅ 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
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files_exist - File found: lib/nfcore_external_java_deps.jar
files_exist - File found: lib/NfcoreTemplate.groovy
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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
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files_exist - File not found check: pipeline_template.yml
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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-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: 23.04.0, Config: 23.04.0
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 (123 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: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: release-announcments.yml
actions_schema_validation - Workflow validation passed: linting.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 2023-10-24 12:56:19

WackerO · 2023-10-23T06:06:45Z

Hey Jonathan, LGTM, but I just noticed while reviewing that I forgot to remove the shinyapp error for maxquant datasets. Can we maybe merge #179 into dev and add to this PR before merging so that this is integrated into the release?

Removed shiny error for proteus runs

nextflow.config

This reverts commit a29351f.

v1.3.0 post-review

pinin4fjords · 2023-10-24T13:09:56Z

Thanks @sateeshperi @WackerO !

Jonathan Manning and others added 30 commits May 1, 2023 17:19

Fix typo from template

035a08f

Co-authored-by: Jasmin Frangenberg <[email protected]>

Merge pull request #124 from healx/merging-template-updates

ebc90fc

Template update for nf-core/tools v2.8

Add spaces to satisfy nf-core download for singularity

d5aa1b2

Update changelog

073ed12

Add explicit rnaseq profile

cbbd88e

Add reviewer

0032fef

Merge pull request #126 from healx/fix_singularity_download2

07543be

Add spaces to satisfy nf-core download for singularity

update

a38a5f0

update

9026637

update

14b822d

added file existence check

3da22bf

Merge pull request #128 from ctuni/master

cdd9d9b

Posible fix for issue #127

Module updates to fit with recent registry changes

fa9b459

Update CHANGELOG

8e24e18

Update reviewers in CHANGELOG

0da403a

Merge pull request #129 from pinin4fjords/container_repos_fix

a7522f3

Module updates to fit with recent registry changes

document reasons for lack of differential expression

4861f7d

correct layout

bfbda94

point on no de

bd92134

prettier

4b2c39f

update changelog

594eb70

Merge branch 'dev' into diff_docs

e43aa3c

Add bug possibility

05a9917

Merge branch 'diff_docs' of github.com:pinin4fjords/differentialabund…

fdda3a2

…ance into diff_docs

Reorder points

e699575

Merge pull request #130 from pinin4fjords/diff_docs

c4995e5

document reasons for lack of differential expression

Make GTF conversion more configurable

b4605cb

Update CHANGELOG

b74e6f2

reprefix gtf options

020aadf

Update modules config for last commit

260d34c

pinin4fjords and others added 17 commits October 17, 2023 16:31

Update CHANGELOG

0e6bce5

[automated] Fix linting with Prettier

ce90d32

Merge pull request #173 from nf-core/deseq2_tip

14e9319

Deseq2 tip

Add missing labels to metro map

390018e

Update CHANGELOG

e6d70bf

Don't use contrasts directly from the input channel

57f32e5

Merge pull request #174 from nf-core/fix_metro_map

46b4d63

Fix metro map

Merge pull request #175 from nf-core/fix_contrasts_usage

f2431bb

Don't use contrasts directly from the input channel

Bump shinyngs versions

d89b142

update changelog

0c90191

poke CI

e8a5519

Correct conda setting

6ff1430

[automated] Fix linting with Prettier

a321afa

Merge pull request #176 from nf-core/bump_shinyngs

763b5e9

Bump shinyngs

Bump versions, tidy up citations, update modules

a82d61d

Clean up after 'nf-core bump-version'

f1643ce

Merge pull request #177 from pinin4fjords/release_v1.3.0

55a6b85

Release v1.3.0

Removed shiny error for proteus runs

99756d4

Merge pull request #179 from WackerO/dev

75f27bc

Removed shiny error for proteus runs

WackerO approved these changes Oct 23, 2023

View reviewed changes

sateeshperi reviewed Oct 24, 2023

View reviewed changes

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sateeshperi approved these changes Oct 24, 2023

View reviewed changes

pinin4fjords added 4 commits October 24, 2023 10:34

remove rogue space

a29351f

bump date

dbc2427

Revert "remove rogue space"

1b09c99

This reverts commit a29351f.

Merge pull request #180 from nf-core/remove_config_space

0d4b452

v1.3.0 post-review

pinin4fjords merged commit e2e2676 into master Oct 24, 2023
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Dev -> master for v1.3.0 #178

Dev -> master for v1.3.0 #178

pinin4fjords commented Oct 19, 2023

github-actions bot commented Oct 19, 2023 •

edited

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❗ Test warnings:

✅ Tests passed:

Run details

WackerO commented Oct 23, 2023

pinin4fjords commented Oct 24, 2023

Dev -> master for v1.3.0 #178

Dev -> master for v1.3.0 #178

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pinin4fjords commented Oct 19, 2023

PR checklist

github-actions bot commented Oct 19, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

WackerO commented Oct 23, 2023

pinin4fjords commented Oct 24, 2023

github-actions bot commented Oct 19, 2023 •

edited

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