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 <jfy133@gmail.com>

Fix multiqc input channels

grst · 2024-08-13T11:30:18Z

👀

#358

This reverts commit 6da0787.

Fix: fb_reference

Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>

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 <jfy133@gmail.com>

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 <12817534+adamrtalbot@users.noreply.github.com>

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

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Release v2.7.1 #356

Release v2.7.1 #356

grst commented Aug 13, 2024

github-actions bot commented Aug 13, 2024 •

edited

Loading

❗ 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

Choose a reason for hiding this comment

jfy133 Aug 13, 2024

Choose a reason for hiding this comment

grst Aug 13, 2024

Choose a reason for hiding this comment

jfy133 Aug 13, 2024

Choose a reason for hiding this comment

grst commented Aug 13, 2024

github-actions bot commented Aug 13, 2024 •

edited

Loading

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