Release v2.7.1 #356

grst · 2024-08-13T05:51:49Z

PR checklist

Bump version to 2.8.0dev

Cellranger 10XV4

Update modules

Fix star index issues

Update modules

Bump version for 2.7.1 release

Re-enable schema linting

Fix usage of getGenomeAttribute

github-actions · 2024-08-13T05:53:24Z

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

Posted for pipeline commit 4f7a09b

+| ✅ 203 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.7.1
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 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 - 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
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: 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: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.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 - EMPTYDROPS_CELL_CALLING 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 - CELLRANGER_MKGTF found in conf/modules.config and Nextflow scripts.
modules_config - CELLRANGER_MKREF found in conf/modules.config and Nextflow scripts.
modules_config - UNIVERSC 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 - 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: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-08-13 14:33:59

jfy133

No blockers from me!

CHANGELOG.md

jfy133 · 2024-08-13T06:07:54Z

workflows/scrnaseq.nf

@@ -67,7 +71,8 @@ workflow SCRNASEQ {
    ch_salmon_index = params.salmon_index ? file(params.salmon_index) : []

    //star params
-    ch_star_index = params.star_index ? file(params.star_index) : []
+    star_index = params.star_index ? file(params.star_index, checkIfExists: true) : null
+    ch_star_index = star_index ? [[id: star_index.baseName], star_index] : []


Is it correct to call this a ch_ prefix when it's not actually in a channel object yet (it seems)?

I'm assuming you're fine with the code, I'm just checking something hasn't been missed

I also use the ch_ prefix for value channels, or basically any variable that is used as a channel and fed into a process.
Are there "official", documented nf-core conventions somewhere?

No, no standards.

Just checking that a channel generation wasn't missing anywhere, where it should have been :)

Co-authored-by: James A. Fellows Yates <[email protected]>

Fix multiqc input channels

grst · 2024-08-13T11:30:18Z

👀

#358

This reverts commit 6da0787.

Fix: fb_reference

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

Fix that tests are not executed

grst and others added 27 commits June 25, 2024 16:18

Bump version to 2.8.0dev

75ba89b

Merge pull request #342 from nf-core/bump-version

6d52c49

Bump version to 2.8.0dev

added 10XV4 for cellranger protocol

e79432c

added v4 whitelist; updated docs for 10XV4

4c93ec0

updated technology pattern

f157de2

updated mandatory_arguments protocol

fbfc780

updated changelog; reverted kallisto meta.yml

e9b20cd

Merge branch 'dev' into cellranger_10XV4

97f8e9b

[automated] Fix code linting

34f4be7

Merge pull request #348 from nick-youngblut/cellranger_10XV4

5f11686

Cellranger 10XV4

Update CHANGELOG

d5d3b98

Update modules

823ef05

Update CHANGELOG

9677a15

Merge pull request #351 from nf-core/update-modules

66221f6

Update modules

Merge branch 'dev' into fix-star-index

e6f282d

Update modules

7a1b851

Update changelog

ecf08e5

Update retrieving star index'

ed25fd5

Merge pull request #350 from nf-core/fix-star-index

23fcbdb

Fix star index issues

Merge pull request #352 from nf-core/update-modules

cafadb9

Update modules

Bump version to v2.7.1

03b9cbc

Merge pull request #353 from nf-core/bump-version

4cd70a1

Bump version for 2.7.1 release

Re-enable schema linting

6da0787

Add missing options to nextflow.config

c918195

Merge pull request #354 from nf-core/fix-linting

0b0ebd4

Re-enable schema linting

Fix usage of getGenomeAttribute

1a683ac

Merge pull request #355 from nf-core/genome-parameters

7baac55

Fix usage of getGenomeAttribute

grst requested review from fmalmeida and nictru August 13, 2024 05:53

jfy133 approved these changes Aug 13, 2024

View reviewed changes

Update CHANGELOG.md

25ed00c

Co-authored-by: James A. Fellows Yates <[email protected]>

mashehu approved these changes Aug 13, 2024

View reviewed changes

grst and others added 3 commits August 13, 2024 12:02

Add missing multiqc channels

bc63dc9

Merge remote-tracking branch 'origin/dev' into fix-multiqc

de7007c

Merge pull request #357 from nf-core/fix-multiqc

2dd8465

Fix multiqc input channels

grst and others added 10 commits August 13, 2024 13:38

rename tests

76c3753

error message when feature barcoding ref is not specified

7582f30

Update nf-test CI and nf-validation plugin

0ce64b1

Fix env vars

7adc979

Revert "Re-enable schema linting"

9a31090

This reverts commit 6da0787.

Update CHANGELOG

7da25ee

Merge pull request #360 from eolaniru/Fixfb_ref

8923d21

Fix: fb_reference

Merge remote-tracking branch 'origin/dev' into fix-nf-test

119c4ba

Update CHANGELOG.md

b1ef5bb

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

Merge pull request #359 from nf-core/fix-nf-test

4f7a09b

Fix that tests are not executed

grst merged commit 4171377 into master Aug 15, 2024
28 checks passed

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Release v2.7.1 #356

Release v2.7.1 #356

grst commented Aug 13, 2024

github-actions bot commented Aug 13, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

jfy133 left a comment

jfy133 Aug 13, 2024

grst Aug 13, 2024

jfy133 Aug 13, 2024

grst commented Aug 13, 2024

Release v2.7.1 #356

Release v2.7.1 #356

Conversation

grst commented Aug 13, 2024

PR checklist

github-actions bot commented Aug 13, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

jfy133 left a comment

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jfy133 Aug 13, 2024

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grst Aug 13, 2024

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jfy133 Aug 13, 2024

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grst commented Aug 13, 2024

github-actions bot commented Aug 13, 2024 •

edited

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