Release candidate 2.1.0 #169

maxulysse · 2023-06-01T12:00:48Z

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/hic 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).

Fixes #150

fixed a few spelling mistakes

Move to v2.1.0dev

Fix incorrect handling of --restriction_site and --ligation_site params

Fixed some spelling mistakes in the Output documentation

…o prefix

Add public_aws_ecr profile for using public ECR images

Important! Template update for nf-core/tools v2.8

conf/test_full.config

maxulysse · 2023-06-01T12:05:08Z

nextflow.config

    mainScript      = 'main.nf'
    nextflowVersion = '!>=22.10.1'
-    version = '2.0.0'
+    version         = '2.1.0dev'


will be updated by #168

maxulysse · 2023-06-01T12:05:31Z

CHANGELOG.md

 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

+## v2.1.0dev


will be updated by #168

This is the typical thing I forget to do before releasing 🤣

I either do 2 PRs, or do it all in one

conf/public_aws_ecr.config

modules/local/hicpro/combine_mates.nf

modules/local/hicpro/get_restriction_fragments.nf

modules/local/hicpro/get_valid_interaction.nf

modules/local/hicpro/get_valid_interaction_dnase.nf

modules/local/hicpro/merge_stats.nf

github-actions · 2023-06-01T12:26:55Z

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

Posted for pipeline commit c3cf64d

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

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.1.0'

✅ 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-hic_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-hic_logo_light.png
files_exist - File found: docs/images/nf-core-hic_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/NfcoreSchema.groovy
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/WorkflowHic.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: 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-hic_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.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
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-hic_logo_light.png matches the template
files_unchanged - docs/images/nf-core-hic_logo_light.png matches the template
files_unchanged - docs/images/nf-core-hic_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 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 (126 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: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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 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 2.8
Run at 2023-06-01 13:34:18

JoseEspinosa

Great job @maxulysse 🚀 !

JoseEspinosa · 2023-06-01T12:25:10Z

CHANGELOG.md

 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

+## v2.1.0dev


This is the typical thing I forget to do before releasing 🤣

Co-authored-by: Adam Talbot <[email protected]>

CHORES: Prepare release

nservant and others added 28 commits January 21, 2023 12:56

[BUMP] v2.1.0dev

eca7e5a

[MODIF] update CHANGELOG

a183052

Fix incorrect handling of --restriction_site and --ligation_site params

f2163ed

Fixes #150

Trigger CI

8893552

Update output.md

fa42adc

fixed a few spelling mistakes

Merge pull request #148 from nservant/dev

53b8b57

Move to v2.1.0dev

Merge pull request #153 from robomics/bugfix

b2a5235

Fix incorrect handling of --restriction_site and --ligation_site params

Merge pull request #155 from jzohren/master

1cc0a18

Fixed some spelling mistakes in the Output documentation

Template update for nf-core/tools version 2.8

7d1306d

Update all NF-Core modules to latest version which includes no quay.i…

16ed196

…o prefix

Add default registry to quay.io

2f11c1d

Update local modules

50ec0d4

quay.io

01d51d5

ubuntu:20.04 to nf-core version

5f8dff5

black

91784a3

Merge pull request #165 from adamrtalbot/update_modules

6e07bfd

Add public_aws_ecr profile for using public ECR images

36974f0

Merge branch 'dev' into public_aws_ecr_profile

aa7ecea

Add BOWTIE2_ALIGN_TRIMMED to use mulled container

88dc793

Update setup-nextflow gha

6785728

Revert linting.yml

fe6b4e7

Merge pull request #166 from adamrtalbot/public_aws_ecr_profile

e44c9ae

Add public_aws_ecr profile for using public ECR images

Merge branch 'dev' into nf-core-template-merge-2.8

cb4d451

prettier

40c8337

bump version

c24f8f8

Merge pull request #159 from nf-core/nf-core-template-merge-2.8

31b66ce

Important! Template update for nf-core/tools v2.8

Merge branch 'dev' into release_2.1.0

a7d9ebd

update version in CHANGELOG

67c5fda

maxulysse commented Jun 1, 2023

View reviewed changes

conf/test_full.config Outdated Show resolved Hide resolved

maxulysse commented Jun 1, 2023

View reviewed changes

conf/test_full.config Outdated Show resolved Hide resolved

Apply suggestions from code review

c55a7fc

maxulysse commented Jun 1, 2023

View reviewed changes

conf/public_aws_ecr.config Outdated Show resolved Hide resolved

Update conf/public_aws_ecr.config

856f949

adamrtalbot approved these changes Jun 1, 2023

View reviewed changes

JoseEspinosa approved these changes Jun 1, 2023

View reviewed changes

maxulysse and others added 2 commits June 1, 2023 14:36

Apply suggestions from code review

57b87d8

Co-authored-by: Adam Talbot <[email protected]>

Merge pull request #168 from maxulysse/release_2.1.0

c3cf64d

CHORES: Prepare release

maxulysse merged commit fe4ac65 into master Jun 1, 2023

Release candidate 2.1.0 #169

Release candidate 2.1.0 #169

Uh oh!

Conversation

maxulysse commented Jun 1, 2023

PR checklist

Uh oh!

Uh oh!

Uh oh!

maxulysse Jun 1, 2023

Choose a reason for hiding this comment

Uh oh!

maxulysse Jun 1, 2023

Choose a reason for hiding this comment

Uh oh!

JoseEspinosa Jun 1, 2023

Choose a reason for hiding this comment

Uh oh!

maxulysse Jun 1, 2023

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

github-actions bot commented Jun 1, 2023 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

Run details

Uh oh!

JoseEspinosa left a comment • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

JoseEspinosa Jun 1, 2023

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

8 participants

github-actions bot commented Jun 1, 2023 •

edited

Loading

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

JoseEspinosa left a comment •

edited

Loading