Release version 4.1.0 of pipeline #485

fmalmeida · 2025-08-01T13:07:18Z

Depends on #484 that contains the commits required for a release that are described in the "Steps for release" section here:
https://nf-co.re/docs/checklists/pipeline_release#steps-to-release

Post steps

After merged, it is required to:

Create a github release: create a new release for your pipeline.
And perform the after release steps.

Outlined at https://nf-co.re/docs/checklists/pipeline_release

…crnaseq into fix_cellrangerarc_input_ch

bumpt dev branch version

Json schema improvements

Change simpleaf protocol name from 10xv4 to 10xv4-3p

updated --cellranger_index docs to point out that the base index directory is needed

Important! Template update for nf-core/tools v3.3.2

Refactor iGenomes handling to expose params object pipeline-wide

github-actions · 2025-08-01T13:09:13Z

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

Posted for pipeline commit 1088423

+| ✅ 248 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  20 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!
schema_description - No description provided in schema for parameter: skip_emptydrops
local_component_structure - gffread_transcriptome.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - star_align.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - alevinqc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - gtf_gene_filter.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - concat_h5ad.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - anndatar_convert.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - mtx_to_h5ad.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - parse_cellrangermulti_samplesheet.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - h5ad_conversion.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - align_cellrangerarc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - kallisto_bustools.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - starsolo.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - simpleaf.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - fastqc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - align_cellrangermulti.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - align_cellranger.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: lib/Utils.groovy
files_exist - File is ignored: tests/default.nf.test
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: .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/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.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: nf-test.config
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 found: ro-crate-metadata.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: 4.1.0
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= simpleaf
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_umi_resolution= cr-like
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/
nf_test_content - 'tests/main_pipeline_cellranger.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_cellranger.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellranger.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_simpleaf.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_simpleaf.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_simpleaf.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_kallisto.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellrangermulti.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_cellrangermulti.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellrangermulti.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellrangermulti.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_cellrangermulti.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellrangermulti.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_star.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_star.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_star.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellrangerarc.nf.test' contains outdir parameter
nf_test_content - 'tests/main_pipeline_cellrangerarc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main_pipeline_cellrangerarc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
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_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.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: 24.10.5, Config: 24.10.5
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
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: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.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 - ANNDATA_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 - 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: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 4.1.0, nfcore_yml.version = 4.1.0
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.3.2
Run at 2025-08-05 07:21:57

Fix nf test version

Bump version 4.1.0 for release

fmalmeida · 2025-08-04T13:41:31Z

Hi @grst ,
Added a small PR for not running conda profile:
#489

exclude conda profile

grst

LGTM

nictru

Looks good :)

fmalmeida · 2025-08-11T09:00:29Z

Hi @grst ,
Do you know why the full sizes are failling? Maybe is not to worry?
I ask because in last PR it seemed that they were skipped:
https://github.com/nf-core/scrnaseq/actions/runs/13765644905

grst · 2025-08-11T09:05:59Z

I have no idea! I would expect full-size tests to run before release, otherwise what's the point.

@nictru, are you aware how this should be?

nictru · 2025-08-11T12:11:43Z

Yes they should run, but I am not too proficient with the full-size tests, so I would ask someone else for help

grst · 2025-08-11T12:15:52Z

@nf-core/ops can you help finding out why the full-sized tests are not running? All I can see is a call to the seqera API that fails without an obvious error message.

nictru · 2025-09-02T19:18:32Z

Hey, the megatests through github actions currently don't work, and there is nothing to fix on the pipeline site. Following this thread I now have access to run the tests directly from seqera platform. Will try to get this running soon

fmalmeida · 2025-09-04T10:43:47Z

Hi @nictru ,
Thanks for the update. Please let us know once you have updates of the runs, so we know if we can release it or not
:)

matbonfanti and others added 30 commits March 4, 2025 17:28

modified samplesheet parsing for cellrangeratac

8be8cd6

process fastq_barcode from input samplesheet

6edee1c

get raw and filtered matrices from cellrangerarc output

4de1e0d

fastq_barcode read through meta

ec5cc94

use file only when meta.fastq_barcode is defined

156991c

Merge branch 'dev' into fix_cellrangerarc_input_ch

801aaf1

Merge branch 'dev' into fix_cellrangerarc_input_ch

c2cc11e

draft of the cellrangerarc test added

980f5c6

Merge branch 'fix_cellrangerarc_input_ch' of github.com:matbonfanti/s…

e65bd57

…crnaseq into fix_cellrangerarc_input_ch

bumpt dev branch version

0575182

Merge pull request #447 from nf-core/bump-dev-branch-version

2cc96be

bumpt dev branch version

Merge branch 'dev' into fix_cellrangerarc_input_ch

17cc26b

Change simpleaf protocol name from 10xv4 to 10xv4-3p

950ed95

Update CHANGELOG.md

5d015ff

update nextflow schema

bc91f60

update changelog

0f8d949

[automated] Fix code linting

932fa1c

Merge pull request #453 from abartlett004/json-schema-improvements

a48193f

Json schema improvements

Merge remote-tracking branch 'origin/dev' into patch

b62abef

Merge pull request #452 from milos7250/patch

adcce05

Change simpleaf protocol name from 10xv4 to 10xv4-3p

added cellrangerarc test

6983615

Merge branch 'dev' into fix_cellrangerarc_input_ch

b2df8c4

updated --cellranger_index docs

23ad77b

Merge branch 'dev' into cellranger_index_docs_update

5ab3ba6

Update CHANGELOG.md

fb3ae40

[automated] Fix code linting

2aacd64

Merge pull request #458 from nick-youngblut/cellranger_index_docs_update

e1fc3dd

updated --cellranger_index docs to point out that the base index directory is needed

Merge branch 'dev' into fix_cellrangerarc_input_ch

0f6bcad

Update protocol documentation

b3dbad3

Prettier

efce2aa

grst and others added 5 commits August 1, 2025 14:10

Merge pull request #474 from nf-core/nf-core-template-merge-3.3.2

2630f93

Important! Template update for nf-core/tools v3.3.2

Merge pull request #483 from nf-core/fix_igenomes_params

c1aefc4

Refactor iGenomes handling to expose params object pipeline-wide

perform nf-core tooling version bump

d3eb239

correct errors highlighted by nf-core lint release

19b8b9b

correct changelog version and add missing information of tempalte update

71f74cc

fmalmeida requested review from apeltzer and grst August 1, 2025 13:07

fmalmeida marked this pull request as draft August 1, 2025 13:07

grst and others added 5 commits August 4, 2025 08:34

Update CHANGELOG

8bd9308

change nf-test function so that pipeline version is not encoded

2d6b8da

update snaps

59de85c

Merge pull request #487 from nf-core/fix-nf-test-version

22a4cb3

Fix nf test version

Merge pull request #484 from nf-core/bump-version-4.1.0

eaabd38

Bump version 4.1.0 for release

fmalmeida marked this pull request as ready for review August 4, 2025 13:32

fmalmeida added the Ready for review label Aug 4, 2025

exclude conda profile

20db7dc

Merge pull request #489 from nf-core/do-not-run-conda-nftest

1088423

exclude conda profile

grst approved these changes Aug 5, 2025

View reviewed changes

fmalmeida requested a review from nictru August 5, 2025 07:27

nictru approved these changes Aug 10, 2025

View reviewed changes

edmundmiller added this to PRs to master Sep 2, 2025

github-project-automation bot moved this to Todo in PRs to master Sep 2, 2025

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Uh oh!

Release version 4.1.0 of pipeline #485

Release version 4.1.0 of pipeline #485

fmalmeida commented Aug 1, 2025

Uh oh!

github-actions bot commented Aug 1, 2025 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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fmalmeida commented Aug 4, 2025

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fmalmeida commented Aug 11, 2025

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fmalmeida commented Sep 4, 2025

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Release version 4.1.0 of pipeline #485

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Release version 4.1.0 of pipeline #485

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fmalmeida commented Aug 1, 2025

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github-actions bot commented Aug 1, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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fmalmeida commented Aug 11, 2025

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github-actions bot commented Aug 1, 2025 •

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