v3.0.0 release #404

grst · 2024-12-09T07:53:13Z

Depends on version bump Bump version for 3.0 release #403

PR checklist

bump version to v2.8dev

Standardize conversion workflow

Remove universc subworkflow from pipeline

github-actions · 2024-12-09T07:55:12Z

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

Posted for pipeline commit 68d2811

+| ✅ 217 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

files_exist - File is ignored: lib/Utils.groovy
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
template_strings - template_strings
schema_params - schema_params

✅ 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: 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-scrnaseq_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-scrnaseq_logo_light.png
files_exist - File found: docs/images/nf-core-scrnaseq_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: 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: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
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: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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: docs/images/nf-core-scrnaseq_logo.png
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/NfcoreTemplate.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowScrnaseq.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
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: validation.help.enabled
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 found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
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 variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
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 manifest.version does not contain dev for release: 3.0.0
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
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.aligner= alevin
nextflow_config - Config default value correct: params.protocol= auto
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.simpleaf_rlen= 91
nextflow_config - Config default value correct: params.star_feature= Gene
nextflow_config - Config default value correct: params.kb_workflow= standard
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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/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-scrnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-scrnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-scrnaseq_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore 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: 24.04.2, Config: 24.04.2
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - CELLBENDER_REMOVEBACKGROUND found in conf/modules.config and Nextflow scripts.
modules_config - ADATA_BARCODES found in conf/modules.config and Nextflow scripts.
modules_config - MTX_TO_H5AD found in conf/modules.config and Nextflow scripts.
modules_config - GTF_GENE_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGER_MKGTF found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGER_MKREF found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGER_COUNT found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGERARC_MKGTF found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGERARC_MKREF found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGERARC_COUNT found in conf/modules.config and Nextflow scripts.
modules_config - GFFREAD_TXP2GENE found in conf/modules.config and Nextflow scripts.
modules_config - SIMPLEAF_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SIMPLEAF_QUANT found in conf/modules.config and Nextflow scripts.
modules_config - ALEVINQC found in conf/modules.config and Nextflow scripts.
modules_config - STAR_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - STAR_GENOMEGENERATE found in conf/modules.config and Nextflow scripts.
modules_config - STAR_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - STAR_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - KALLISTOBUSTOOLS_REF found in conf/modules.config and Nextflow scripts.
modules_config - KALLISTOBUSTOOLS_COUNT found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - NFCORE_SCRNASEQ found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGER_MKGTF found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGER_MKREF found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGER_MKVDJREF found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2
version_consistency - Version tags are numeric and consistent between container, release tag and config.
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.0.2
Run at 2024-12-10 10:30:17

Bump version for 3.0 release

fmalmeida · 2024-12-09T09:36:58Z

Hi @grst ,
I am launching some test_full runs just to guarantee
:)

Better readme statement

fmalmeida · 2024-12-10T08:20:09Z

Hi @grst , I am launching some test_full runs just to guarantee :)

Hi @grst ,
I have found a problem with kallisto NAC workflow. Which I forgot to include its correct file names.

I am going to fix it in https://github.com/nf-core/scrnaseq/tree/fix-kallisto-nac-in-v300 then would be ready.

include nac conversion workflow

fmalmeida

After fixing the nac workflow with #406 , now my full tests are running fine.
So, I think it looks good for merge.

apeltzer · 2024-12-10T12:48:43Z

Someone else should do the release ;-)

grst and others added 30 commits August 15, 2024 08:29

bump version to v2.8dev

4c27011

update changelog

3aaf168

Merge pull request #362 from nf-core/bump-version

783510f

bump version to v2.8dev

comment out for development

52fa9ca

refact modules for STAR aligner

bbf299c

directly pass txp2gene

c3eb5ea

simplify module lines

4771ed1

emit h5ad on starsolo

af85f87

add versions emition

d2a5386

update module to use templates and cleanup way of priting versions

0e55051

fix h5ad generator script

994d5a5

simplify check

b317165

Fix h5ad structure

72e9d50

updated concat module

8829080

workflow misses emptydrops and seurat & mtx conversion modules

9fc75b4

start emptydrops cellbender subworkflow

dc69f47

fix paths

9c20420

started the anndatar standardization module

6831195

concat h5ad with anndatar h5ad

237d1ca

update tag information

f5fb4a2

update tags

752666b

module is only to convert to rds

d0ad7f6

update directives

20ac4ae

update comments

da5b036

add cellbender to workflow

b90f388

start organisation of files

7c304cc

update doc related to alevin-fry, simpleaf and salmon

012f608

update simpleaf reference

c02a054

change aligner name back to alevin

f2c1a24

change aligner name back to alevin

77f91f7

fmalmeida and others added 15 commits November 29, 2024 14:20

add metadata

d194bfa

allow regex to also find cellrangermulti results

e9836fd

update cellranger multi nf-test snaps

3e3608c

update star nf-test snaps

2830093

prettier fix

fae53a2

avoid fetching star index from iGenomes due version incompatibility

84a83c2

add .var_names_make_unique() to star code which was missing

b498ddc

Merge pull request #369 from nf-core/standardize-conversion-workflow

d3d8a6f

Standardize conversion workflow

update changelog

ba38a9c

remove all universc things

0a48157

update images

8a98f31

use correct java version in ci

5aa3068

Merge pull request #396 from nf-core/289-update-or-remove-universc

c336812

Remove universc subworkflow from pipeline

bump version and update changelog

6878b6b

enable custom pipeline config

eaca45a

grst requested a review from fmalmeida December 9, 2024 07:54

Merge pull request #403 from nf-core/bump-version

1a84433

Bump version for 3.0 release

fmalmeida requested a review from apeltzer December 9, 2024 09:37

Improved statement regarding 10X container(s)

ffe4ae2

apeltzer approved these changes Dec 9, 2024

View reviewed changes

Merge pull request #405 from nf-core/licence-readme

5209fe4

Better readme statement

include nac conversion workflow

e00f98c

fmalmeida mentioned this pull request Dec 10, 2024

include nac conversion workflow #406

Merged

Merge pull request #406 from nf-core/fix-kallisto-nac-in-v300

68d2811

include nac conversion workflow

fmalmeida approved these changes Dec 10, 2024

View reviewed changes

apeltzer merged commit 89a7986 into master Dec 10, 2024
33 checks passed

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v3.0.0 release #404

v3.0.0 release #404

grst commented Dec 9, 2024 •

edited by fmalmeida

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github-actions bot commented Dec 9, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

fmalmeida commented Dec 9, 2024

fmalmeida commented Dec 10, 2024

fmalmeida left a comment

apeltzer commented Dec 10, 2024

v3.0.0 release #404

v3.0.0 release #404

Conversation

grst commented Dec 9, 2024 • edited by fmalmeida Loading

PR checklist

github-actions bot commented Dec 9, 2024 • edited Loading

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

fmalmeida commented Dec 9, 2024

fmalmeida commented Dec 10, 2024

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apeltzer commented Dec 10, 2024

grst commented Dec 9, 2024 •

edited by fmalmeida

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github-actions bot commented Dec 9, 2024 •

edited

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