Release 2.1.0 #97

Daniel-VM · 2023-10-23T10:05:46Z

PR description

This PR is for release 2.1.0

Major changes are:
- nf-core/bacass update to nf-core tools 2.10
- Refactor local modules into nf-core modules when possilbe (plus version update).
- Added nf-core subworkflow for trimming and QC using FastP and fastqc, respectively
- Added nf-validation pluging on samplesheet.
- Added module's output statistics to MultiQC.
- Added subworkflow for gene annotation with Bakta

More details in CHANGLEOG

Note: You will see two commits that bump versions >2.1.0. Those were my mistakes and there were fixed in #95 to recover v2.1.0.

PR checklist

Merging template updates 2.9 and workflow update

nf-validation on samplesheet

Add new module for gene annotation: Bakta

Prepare release 2.1.0

github-actions · 2023-10-23T10:08:01Z

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

Posted for pipeline commit c005ee3

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

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

❔ Tests ignored:

files_exist - File is ignored: conf/igenomes.config

✅ 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-bacass_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-bacass_logo_light.png
files_exist - File found: docs/images/nf-core-bacass_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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowBacass.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-bacass_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-bacass_logo_light.png matches the template
files_unchanged - docs/images/nf-core-bacass_logo_light.png matches the template
files_unchanged - docs/images/nf-core-bacass_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 (126 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/tsv'
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 2023-10-23 16:41:51

d4straub

Looks good to me! (but I also reviewed the individual PRs, so not a big surprise)

For a release (i.e. PR to master from dev) are 2 reviews necessary. You could post a request to get reviews in nf-core slack #request-review.

edit: additionally, required tests are also blocking the merge, I requested a change of branch protection rules in nf-core slack channel pipeline-maintainers.

Daniel-VM · 2023-10-23T10:41:50Z

Ok ;). Thanksss @d4straub !

Daniel-VM · 2023-10-23T13:21:35Z

Should I commit a dummy change directly to nf-core/bacass:dev (my upstream) to reset the GitHub test? Or would it be better to push to my fork (dev) and then merge the forked dev into nf-core/bacass:dev?

d4straub · 2023-10-23T14:11:30Z

Not sure. Whatever works. Might closing and re-opening of this PR work (not sure)?

d4straub · 2023-10-23T14:34:18Z

Unfortunately it didnt update the tests, so it seems to need a push. Sorry (but would have been the quickest fix...).

Daniel-VM · 2023-10-23T14:40:06Z

I see 😅, we had to try it. I am going to add a new commit and see if it updates the tests.

dummy change to update github test #97

d4straub · 2023-10-23T16:44:16Z

Hm, but Run pipeline with test data is still expected but it shouldn't!!! I assume the branch protection isn't fixed yet... :'(

d4straub and others added 30 commits August 27, 2021 14:41

bump version to 2.1.0dev

7177a4f

Merge pull request #62 from d4straub/dev

d96132a

Template update for nf-core/tools version 2.2

114f6b0

Template update for nf-core/tools version 2.3

3b846ba

Template update for nf-core/tools version 2.3.1

3e5ae0d

Template update for nf-core/tools version 2.3.2

ecf6fbb

Template update for nf-core/tools version 2.4

270849a

Template update for nf-core/tools version 2.5

2c8a2a7

Template update for nf-core/tools version 2.5.1

8d72268

Template update for nf-core/tools version 2.6

152aed3

Template update for nf-core/tools version 2.7.1

3a8ff0b

Template update for nf-core/tools version 2.7.2

1013466

Template update for nf-core/tools version 2.8

8395089

Template update for nf-core/tools version 2.9

73a07e9

reslove conflict after nf-core template-2.9 update

63cc816

fix nf-core linting

cd125df

fix editorConfig

686279d

fix prettier typo

3858449

fix CI test

a1fc98a

Fix missing snippet while merging conflicts

61d4761

make patch to Nanoplot

c9dbfcc

Apply suggestios from code reviewer

715b86a

fix prettier after adding code-reviewer suggestions

3abc9ed

removed lines causing warnings

5c6fbee

Merge pull request #86 from Daniel-VM/dev

ba415ef

Merging template updates 2.9 and workflow update

fix doc samplesheet file extension

7508612

update access to test datasets

d88c7e1

add nf-validation on samplesheet

d512b45

add reviewer suggestions

8ba1df5

Merge pull request #88 from Daniel-VM/dev

463d4b0

nf-validation on samplesheet

Daniel-VM and others added 16 commits October 16, 2023 17:50

update documentation bakta

3bd173a

new output organisation for bakta

08b81ea

remove warning message baktadbdowload

5a00a68

downgrade baktadbdownload to overcome dependency conflicts

f65582b

prettier fix

e01d0fe

fix minor typo

4aefaf6

bump version v2.1.2dev

4004177

update multiqc to v1.17

d0c4f8b

update changelog #95

14761cc

add reviewer suggestions #95

3c79c45

Merge pull request #95 from Daniel-VM/dev

6bd6045

Add new module for gene annotation: Bakta

fix changelog in v2.1.0dev

a61c9b7

bumpversion and update changelog

a1e98a2

eliminate unnecesary TODOs

266002a

fix console indentation

84b58ac

Merge pull request #96 from Daniel-VM/dev

3f6d59b

Prepare release 2.1.0

d4straub approved these changes Oct 23, 2023

View reviewed changes

Daniel-VM closed this Oct 23, 2023

Daniel-VM reopened this Oct 23, 2023

dummy change to update github test #97

235d377

Daniel-VM mentioned this pull request Oct 23, 2023

dummy change to update github test #97 #98

Merged

10 tasks

Merge pull request #98 from Daniel-VM/dev

c005ee3

dummy change to update github test #97

mashehu merged commit e94a173 into master Oct 23, 2023
21 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Release 2.1.0 #97

Release 2.1.0 #97

Daniel-VM commented Oct 23, 2023 •

edited

Loading

github-actions bot commented Oct 23, 2023 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

d4straub left a comment •

edited

Loading

Daniel-VM commented Oct 23, 2023

Daniel-VM commented Oct 23, 2023 •

edited

Loading

d4straub commented Oct 23, 2023

d4straub commented Oct 23, 2023

Daniel-VM commented Oct 23, 2023

d4straub commented Oct 23, 2023

Release 2.1.0 #97

Release 2.1.0 #97

Conversation

Daniel-VM commented Oct 23, 2023 • edited Loading

PR description

PR checklist

github-actions bot commented Oct 23, 2023 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

d4straub left a comment • edited Loading

Choose a reason for hiding this comment

Daniel-VM commented Oct 23, 2023

Daniel-VM commented Oct 23, 2023 • edited Loading

d4straub commented Oct 23, 2023

d4straub commented Oct 23, 2023

Daniel-VM commented Oct 23, 2023

d4straub commented Oct 23, 2023

Daniel-VM commented Oct 23, 2023 •

edited

Loading

github-actions bot commented Oct 23, 2023 •

edited

Loading

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

d4straub left a comment •

edited

Loading

Daniel-VM commented Oct 23, 2023 •

edited

Loading