Release v2.6.0 #318

grst · 2024-04-16T12:37:44Z

PR checklist

bump version and update changelog

…lement-tests-with-nf-test

Bump version to 2.6.0dev

tested only with kallisto aligner (both with and without automated kallisto filtering with bustools --filter parameter)

…(tested with lamanno)

That is not really what this argument does – it just concatenates the gene_version and transcript_version fields to IDs.

The txp2gene file should really be generated by kallisto|bustools. The t2g.py script generates a 3-column rather than 7-column t2g, which seems to be incompatible with kb count.

This .collect() is incompatible with passing in an existing t2g, and superfluous given the .collect() after the kb ref call.

t1c and t2c are required to run nac and lamanno count workflows. Since they are already defined when running kb ref, they cannot be easily defined through ext.args when using an existing reference

scrnaseq does not actually use kallisto_gene_map anywhere. Changed kallisto icon from a salmon to a rainbow (there is no bear icon, but bustools uses the Pink Floyd-esque prism image, so it seems most appropriate)

Fix issue 81, "call empty droplets"

…-latest-nf-coremodules-versions 316 update cellranger modules to latest nf coremodules versions

github-actions · 2024-04-16T12:39:40Z

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

Posted for pipeline commit 7be5e57

+| ✅ 170 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.6.0
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: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
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-scrnaseq_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: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowScrnaseq.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
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
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.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
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
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
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_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: awstest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.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: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.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' 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'

Run details

nf-core/tools version 2.13.1
Run at 2024-04-30 12:00:21

Bump version to 2.6.0

subworkflows/local/mtx_conversion.nf

Add cellrangerarc snippet back

fmalmeida

Now that the comment here was resolved and we brought the cellrangerarc snippet back to avoid un-tested errors.

I think it looks good summed with the passing tests.

LaurenceKuhl

hey LGTM :)

fmalmeida and others added 30 commits January 19, 2024 11:40

add nf-test for alevin aligner

739fbb5

adding nf-test for star aligner

23072dc

Merge branch 'dev' of https://github.com/nf-core/scrnaseq into 91-imp…

c65e134

…lement-tests-with-nf-test

first commit: bump up kb versions

19132ff

Bump version to 2.6.0dev

8037005

Merge pull request #295 from nf-core/bump-version

ddf3e1d

Bump version to 2.6.0dev

add nf-tests for cellranger aligner

4ae28e3

add nf-test for kallisto aligner

b56577c

Merge branch 'nf-core:master' into kb_update

9e176ac

Template update for nf-core/tools version 2.12

7a01c5b

renaming parameters

4ef499e

Memory arg might need to be before fastq list?

fb6db73

Update main.nf

3ccd083

minimum inclusion for module

6d81894

tested only with kallisto aligner (both with and without automated kallisto filtering with bustools --filter parameter)

update input_type labels

afe4904

Fixing issue #297

59648cc

fixed workflow conversions to work with star align results

d03d81f

fix issue 299

3324a78

Fix for Issue 229

f938744

include modifications for working with cellranger

796afba

fix the path of matrices when running non-standard kallisto workflow …

c9c38ea

…(tested with lamanno)

fix spliced/unspliced empty_drops conversion

a9ee3f1

solve number of list levels when having spliced / unspliced

0cb2a2f

Removed t2g versions call

45e0b19

That is not really what this argument does – it just concatenates the gene_version and transcript_version fields to IDs.

removing t2g.py

50d3948

The txp2gene file should really be generated by kallisto|bustools. The t2g.py script generates a 3-column rather than 7-column t2g, which seems to be incompatible with kb count.

Remove txp2gene.collect() call

b0d7c5d

This .collect() is incompatible with passing in an existing t2g, and superfluous given the .collect() after the kb ref call.

add t1c/t2c parameters to schema

8630ef9

t1c and t2c are required to run nac and lamanno count workflows. Since they are already defined when running kb ref, they cannot be easily defined through ext.args when using an existing reference

Fixed kallisto_gene_map documentation

e503e21

scrnaseq does not actually use kallisto_gene_map anywhere. Changed kallisto icon from a salmon to a rainbow (there is no bear icon, but bustools uses the Pink Floyd-esque prism image, so it seems most appropriate)

Update nextflow_schema.json

752d051

Merge branch 'dev' into nf-core-template-merge-2.12

8d077d9

fmalmeida and others added 12 commits March 18, 2024 14:07

update modules to get them from nf-core/modules

c460f28

prettier fix

1c1f1ac

small update as file names changed

6351f76

add ending line

9734ace

update changelog

2406600

Merge pull request #301 from nf-core/81-call-empty-droplets

1043441

Fix issue 81, "call empty droplets"

updated modules with 'nf-core modules update'

8802cd9

update changelog

6dc725b

parse filtered / raw channels

95a9ffa

update nf-test snaps

f0b309f

default to true

984c101

Merge pull request #317 from nf-core/316-update-cellranger-modules-to…

7c15e0a

…-latest-nf-coremodules-versions 316 update cellranger modules to latest nf coremodules versions

grst and others added 4 commits April 16, 2024 14:48

bump version and update changelog

5b3796f

Update download_pipeline.yml

c1e98b3

[automated] Fix linting with Prettier

4efe296

Merge pull request #320 from nf-core/release-2.6.0

6a7d203

Bump version to 2.6.0

grst requested a review from fmalmeida April 18, 2024 08:27

fmalmeida requested a review from apeltzer April 19, 2024 11:27

fmalmeida reviewed Apr 19, 2024

View reviewed changes

subworkflows/local/mtx_conversion.nf Show resolved Hide resolved

re-added celranger-arc backwards compatibility

900606f

fmalmeida mentioned this pull request Apr 30, 2024

Add cellrangerarc snippet back #321

Merged

Merge pull request #321 from nf-core/add-cellrangerarc-snippet-back

7be5e57

Add cellrangerarc snippet back

fmalmeida assigned grst Apr 30, 2024

fmalmeida added enhancement New feature or request Ready for review labels Apr 30, 2024

fmalmeida approved these changes Apr 30, 2024

View reviewed changes

fmalmeida requested a review from maxulysse May 6, 2024 09:00

LaurenceKuhl approved these changes May 7, 2024

View reviewed changes

grst merged commit c5a6445 into master May 7, 2024
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Release v2.6.0 #318

Release v2.6.0 #318

grst commented Apr 16, 2024 •

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github-actions bot commented Apr 16, 2024 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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fmalmeida left a comment •

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LaurenceKuhl left a comment

Release v2.6.0 #318

Release v2.6.0 #318

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grst commented Apr 16, 2024 • edited Loading

PR checklist

github-actions bot commented Apr 16, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

fmalmeida left a comment • edited Loading

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grst commented Apr 16, 2024 •

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github-actions bot commented Apr 16, 2024 •

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

fmalmeida left a comment •

edited

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