Dev -> master for v1.2.0 #112

pinin4fjords · 2023-04-19T09:32:18Z

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).

Bump versions after 1.1.1 bugfix release

Warn missing gene sets

use color scales appropriate to variable, apply upstream palette fixes

…ions

Update differential module interface, add pre-contrast subsetting options

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

This reverts commit faacf06.

This reverts commit d2eaf06.

Add shinyngs app creation and deployment

Add shinyngs outputs to Tower reports

Co-authored-by: James A. Fellows Yates <[email protected]>

Release v1.2.0

github-actions · 2023-04-19T09:33:51Z

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

Posted for pipeline commit f7ec824

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '1.2.0'

✅ Tests passed:

files_exist - File found: .gitattributes
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files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
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files_exist - File found: CITATIONS.md
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files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
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files_exist - File found: .github/.dockstore.yml
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files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-differentialabundance_logo_light.png
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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/WorkflowDifferentialabundance.groovy
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files_exist - File not found check: Singularity
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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 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 - .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
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files_unchanged - assets/email_template.txt matches the template
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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/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
readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (111 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
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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 2.7.2
Run at 2023-04-19 16:52:30

assets/differentialabundance_report.Rmd

maxulysse

<3

README.md

nextflow_schema.json

Pre v1.2.0 fixes

pinin4fjords · 2023-04-19T17:44:13Z

Thanks for review @maxulysse @WackerO

Jonathan Manning and others added 30 commits March 3, 2023 08:32

Bump versions after 1.1.1 bugfix release

d1adec2

Merge pull request #92 from healx/v1.1.1_post_release

f25c482

Bump versions after 1.1.1 bugfix release

make color palette specific to variables under consideration

1d18f34

Actually use dendrocolorscale

86146f2

Update CHANGELOG

346888b

Exit workflow if gene sets not supplied for GSEA

9dd3242

Update changelog

2ec3fee

dummy commit for CI

9eb4c64

exits -> exceptions

25226d7

Add reviewer to CHANGELOG

c18db01

Bump shinyngs version used for notebook

97957f1

Run prettier

8b6c9ed

throw -> error()

fb1c2ec

Correct CHANGELOG formatting

f38476f

Bump shinyngs modules

6c63275

Bump shinyngs again in markdown

94dec85

Merge pull request #96 from healx/warn_missing_gene_sets

c65406e

Warn missing gene sets

Merge branch 'dev' into more_color_scale_fixes

686fab3

Merge pull request #94 from healx/more_color_scale_fixes

e527167

use color scales appropriate to variable, apply upstream palette fixes

Update differential module interface, add pre-contrast subsetting opt…

76b848c

…ions

Update CHANGELOG

e25afc5

Appease eclint

ce775ec

Merge pull request #103 from healx/subset_for_differential

5c4a04e

Update differential module interface, add pre-contrast subsetting options

Enabled multiple GMT/GMX files for GSEA

9f05314

Update nextflow_schema.json

ff8f658

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

Update workflows/differentialabundance.nf

45682a4

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

Update workflows/differentialabundance.nf

dcb30c1

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

Update workflows/differentialabundance.nf

1eb045c

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

Update conf/modules.config

18bad35

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

Update workflows/differentialabundance.nf

93f014b

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

Jonathan Manning and others added 19 commits April 8, 2023 19:37

install shinyngs modules properly after modules PR

fc4ca54

Revert "install shinyngs modules properly after modules PR"

b812227

This reverts commit faacf06.

Renable app generation for affy arrays now there's a fix upstream

35014ae

Remove function moved upstream

5962e5a

patch while we wait for pinin4fjords/shinyngs#44 to release upstream

d4f3e48

Add reviewer

cdee427

Wire in markdown report to app generation

d2eaf06

Revert "Wire in markdown report to app generation"

b1ffa16

This reverts commit d2eaf06.

Merge pull request #107 from healx/add_shinyngs_app

ffc10b0

Add shinyngs app creation and deployment

Add shiny app outputs to Tower reports

e6d16f0

Update changelog

e36656c

dummy commit

3276e2e

Add reviewers to changelog

9a66c9f

Fix changelog formatting

30247f9

Merge pull request #110 from healx/shinyngs_tower_yml

5e3e742

Add shinyngs outputs to Tower reports

Pre-release changes for 1.2.0

52c351d

Dummy commit after PR base fix

f4c7cb1

fix version indent

1a8154d

Co-authored-by: James A. Fellows Yates <[email protected]>

Merge pull request #111 from healx/release_v1.2.0

d14507e

Release v1.2.0

pinin4fjords commented Apr 19, 2023

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maxulysse approved these changes Apr 19, 2023

View reviewed changes

pinin4fjords commented Apr 19, 2023

View reviewed changes

README.md Outdated Show resolved Hide resolved

pinin4fjords commented Apr 19, 2023

View reviewed changes

nextflow_schema.json Outdated Show resolved Hide resolved

Fix typos

abc3576

WackerO approved these changes Apr 19, 2023

View reviewed changes

Jonathan Manning added 2 commits April 19, 2023 14:37

Dummy commit for CI

217e907

Merge pull request #113 from healx/pre_v1.2.0_fixes

f7ec824

Pre v1.2.0 fixes

pinin4fjords merged commit 3a849f0 into master Apr 19, 2023

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Dev -> master for v1.2.0 #112

Dev -> master for v1.2.0 #112

pinin4fjords commented Apr 19, 2023

github-actions bot commented Apr 19, 2023 •

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❗ Test warnings:

✅ Tests passed:

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maxulysse left a comment

pinin4fjords commented Apr 19, 2023

Dev -> master for v1.2.0 #112

Dev -> master for v1.2.0 #112

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pinin4fjords commented Apr 19, 2023

PR checklist

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

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

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pinin4fjords commented Apr 19, 2023

github-actions bot commented Apr 19, 2023 •

edited

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