Release v2.5.0 #283

grst · 2024-01-02T12:14:49Z

v2.5.0 - 2024-01-02

Update template to v2.11.1 (#279)
Add support for paired GEX+ATAC sequencing using cellranger-arc (#274)
Increase default runtime limits for all processes ([increase time limits #281])(increase time limits #281)
Better support for custom protocols (#273).
- The universc protocol is now specified via the --protocol flag
- Any protocol specified is now passed to the respective aligner
- Added a section to the documentation

PR checklist

Bump version to 2.5.0dev

Better support for custom chemistries

Adding cellranger-arc (multiome scRNA-seq + scATAC support)

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

increase time limits

bump version to 2.5.0 for release

github-actions · 2024-01-02T12:16:36Z

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

Posted for pipeline commit d6329ee

+| ✅ 161 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.5.0

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
template_strings - template_strings

✅ 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-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
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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: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowScrnaseq.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-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: .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
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 - 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
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: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.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 2.11.1
Run at 2024-01-08 15:38:27

fmalmeida · 2024-01-03T17:56:56Z

Hi @grst ,

Currently I am on vacation without my pc. I can take a look once I get back end of next week if no one else had reviewed it yet

😁

grst · 2024-01-03T18:09:17Z

No worries, I feel I'm the only one who's not on vacation this week (which is also why I have time to work on nf-core stuff)

ggabernet

I just have a comment regarding the resources specification in the base.config, otherwise looks good to me!

conf/base.config

This reverts commit 49cfbd5.

heylf

I had a look the only comment I would have is if it would be possible to put under the contribution the GHGA (https://www.ghga.de)? This would help us to make clear where we are involved and where we made progress for the project.

Fix time limits

grst · 2024-01-08T06:58:26Z

I had a look the only comment I would have is if it would be possible to put under the contribution the GHGA (https://www.ghga.de)? This would help us to make clear where we are involved and where we made progress for the project.

of course, just submit a PR with the changes you'd like!

bin/check_samplesheet.py

maxulysse · 2024-01-08T07:06:28Z

lib/WorkflowScrnaseq.groovy

+    public static Map getProtocol(workflow, log, aligner, protocol) {
+        def jsonSlurper = new JsonSlurper()
+        def json = new File("${workflow.projectDir}/assets/protocols.json").text
+        def protocols = jsonSlurper.parseText(json)
+        def aligner_map = protocols[aligner]
+        if(aligner_map.containsKey(protocol)) {
+            return aligner_map[protocol]
+        } else {
+            log.warn("Protocol '${protocol}' not recognized by the pipeline. Passing on the protocol to the aligner unmodified.")
+            return ["protocol": protocol]
        }


I'm impressed

maxulysse

Nothing to add from what was already said

heylf · 2024-01-08T15:28:12Z

I added in this PR the GHGA contribution: #286

GHGA contribution to README

ggabernet

Looks good to me now!

heylf and others added 30 commits June 30, 2023 11:20

Changes to check_samplesheet

2db5cea

Changes to nextflow.config

d197871

Changes to input_check

f36d7fb

Changes to scranseq.nf

beeca28

Adding script for config and lib.csv generation

ee520a5

Adding cellranger-arc modules

87716ed

Adding cellranger-arc subworkflow

57e590c

Adding cellrangerarc to nextflow schema

6ba3042

Adding cellrangerarc to modules.config

ef4b284

Removing genrate lib csv module

5c51b1d

Rename cellrangerarc subworkflow

0b86e18

update cellrangerarc modules

4b343d7

Adding generate config workflow and align cellrangerarc subworkflow

68a2654

Updating mtx conversion scripts

a81849c

Changing module.config and nextflow.config

f7c07a4

Changing scripts for the input check

bf180da

Bugfix for generate config python script

4d4ed84

Changing multiqc and dumsoftware scripts for containers

cad9024

Changing concat_h5ad.nf

37e61d6

Changing gtf_gene_filter.nf

f884d00

Chaning scrnaseq.nf

fe187a6

Bump version to 2.5.0dev

f9f581e

Merge pull request #271 from nf-core/bump-version

ac11e3c

Bump version to 2.5.0dev

Update nextflow schema and switch to protocol mapping via JSON

0cbe7c6

Support protocol in all aligners

ad5e8ba

Update documentation

9a619ec

Update changelog

386bcfd

Fix syntax error

41f1481

Fix prettier

af63d84

Merge pull request #273 from nf-core/custom-chemistries

2a853c9

Better support for custom chemistries

grst and others added 8 commits December 22, 2023 07:58

Merge pull request #274 from heylf/cellrangerarc

bf280ce

Adding cellranger-arc (multiome scRNA-seq + scATAC support)

Increase time limits

49cfbd5

trigger ci

cc3aa97

Update Changelog

9df519a

Update CHANGELOG.md

31ea547

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Merge pull request #281 from nf-core/increase-time-limits

8583e5c

increase time limits

bump version to 2.5.0 for release

f0d08ac

Merge pull request #282 from nf-core/bump-version

f97a466

bump version to 2.5.0 for release

grst requested review from heylf and fmalmeida January 2, 2024 12:15

ggabernet requested changes Jan 4, 2024

View reviewed changes

conf/base.config Outdated Show resolved Hide resolved

grst added 3 commits January 5, 2024 14:21

Revert "Increase time limits"

584ddf6

This reverts commit 49cfbd5.

Move increased runtime limits from base.config to modules.config

b5bcedb

Update changelog

bc8825a

heylf reviewed Jan 5, 2024

View reviewed changes

Merge pull request #284 from nf-core/fix-time-limits

2398f98

Fix time limits

maxulysse reviewed Jan 8, 2024

View reviewed changes

bin/check_samplesheet.py Outdated Show resolved Hide resolved

maxulysse reviewed Jan 8, 2024

View reviewed changes

maxulysse approved these changes Jan 8, 2024

View reviewed changes

grst mentioned this pull request Jan 8, 2024

Use nf-validation plugin #285

Closed

heylf added 2 commits January 8, 2024 16:24

Adding GHGA contribution

04aadab

Adding GHGA contribution

e7f0175

Merge pull request #286 from heylf/dev

d6329ee

GHGA contribution to README

ggabernet approved these changes Jan 9, 2024

View reviewed changes

grst merged commit e03cd46 into master Jan 10, 2024
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Release v2.5.0 #283

Release v2.5.0 #283

grst commented Jan 2, 2024 •

edited

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github-actions bot commented Jan 2, 2024 •

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

fmalmeida commented Jan 3, 2024

grst commented Jan 3, 2024

ggabernet left a comment

heylf left a comment

grst commented Jan 8, 2024

maxulysse Jan 8, 2024

maxulysse left a comment

heylf commented Jan 8, 2024

ggabernet left a comment

Release v2.5.0 #283

Release v2.5.0 #283

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grst commented Jan 2, 2024 • edited Loading

v2.5.0 - 2024-01-02

PR checklist

github-actions bot commented Jan 2, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

fmalmeida commented Jan 3, 2024

grst commented Jan 3, 2024

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grst commented Jan 8, 2024

maxulysse Jan 8, 2024

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grst commented Jan 2, 2024 •

edited

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github-actions bot commented Jan 2, 2024 •

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