Make release by delfiterradas · Pull Request #158 · nf-core/nanostring

delfiterradas · 2026-01-29T15:38:33Z

Closes #157

PR checklist

Updated R package versions in environment.yml for compatibility.

Updated CHANGELOG to reflect recent fixes and dependency changes.

Updates r packages & uses wave for container(s)

Last fix for strict-syntax I guess

github-actions · 2026-01-29T15:40:15Z

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

Posted for pipeline commit 00102db

+| ✅ 217 tests passed       |+
#| ❔   2 tests were ignored |#

Details

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml

✅ 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-nanostring_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-nanostring_logo_light.png
files_exist - File found: docs/images/nf-core-nanostring_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: tests/default.nf.test
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-nanostring_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/Utils.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/WorkflowNanostring.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: 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 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 variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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: 1.3.3
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.heatmap_id_column= SAMPLE_ID
nextflow_config - Config default value correct: params.normalization_method= GEO
nextflow_config - Config default value correct: params.gene_score_method= plage.dir
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
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/test.nf.test' contains outdir parameter
nf_test_content - 'tests/test.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_samples.nf.test' contains outdir parameter
nf_test_content - 'tests/test_samples.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_samples.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_scores.nf.test' contains outdir parameter
nf_test_content - 'tests/test_scores.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_scores.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/bug_report.yml 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/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.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-nanostring_logo_light.png matches the template
files_unchanged - docs/images/nf-core-nanostring_logo_light.png matches the template
files_unchanged - docs/images/nf-core-nanostring_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: 25.10.2, Config: 25.10.2
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
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
template_strings - Did not find any Jinja template strings (0 files)
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: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - NACHO_QC found in conf/modules.config and Nextflow scripts.
modules_config - NACHO_NORMALIZE found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_ANNOTATED_TABLES found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_GENE_HEATMAP found in conf/modules.config and Nextflow scripts.
modules_config - COMPUTE_GENE_SCORES found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC 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: 3.5.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 1.3.3, nfcore_yml.version = 1.3.3
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.5.1
Run at 2026-01-30 14:32:32

assets/multiqc_config.yml

nextflow.config

CHANGELOG.md

Fix version and changelog for release

modules/local/compute_gene_scores/main.nf

CHANGELOG.md

apeltzer · 2026-01-30T10:41:23Z

PR #161 addresses all review comments and also fixes the dependencies for the other two modules + uses https urls for singularity containers there too

Address review comments

Update snapshots

CHANGELOG.md

delfiterradas · 2026-01-30T13:55:10Z

PR #164 should fix the failing tests

Update snapshots

atrigila

Looks good to me now, thanks!

apeltzer and others added 22 commits January 26, 2026 14:06

Last fix for strict-syntax I guess

fcecce5

Update version to 1.3.3dev in nextflow.config

4c76bde

test: update snapshots

697037b

style: fix linting

e18909c

Update R package versions in environment.yml

c20583e

Updated R package versions in environment.yml for compatibility.

Update containers for compute-gene-scores

3019dfd

Simplify container definition in COMPUTE_GENE_SCORES

3741a36

Improve local methods

12263b8

Fix container url

29c66ba

Added in utils update

f5297e1

Adding in construction of params object

582b3a6

Another fix for GSVA

0cebde8

Applied R / AIR formatting

e4bf4e2

Adjusting samsscore

0b2b102

Remove assert that package

6805648

Fix test snap

ff21ede

Typo again

5d237d7

Fix in subworkflow too

5751fd9

Remove trailing whitespace

d4a7cc0

Updated CHANGELOG to reflect recent fixes and dependency changes.

Merge pull request #156 from nf-core/fix-help-1

f3781de

Updates r packages & uses wave for container(s)

update snapshot

57ad22c

Merge pull request #155 from nf-core/fix-help

9b92bf8

Last fix for strict-syntax I guess

delfiterradas self-assigned this Jan 29, 2026

apeltzer reviewed Jan 29, 2026

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CHANGELOG.md Show resolved Hide resolved

delfiterradas and others added 4 commits January 29, 2026 17:15

Bump version

8bfe36a

Fix version and changelog

295aaaa

Update snapshots

59a06ff

Merge pull request #159 from delfiterradas/release

d139c2a

Fix version and changelog for release

atrigila reviewed Jan 29, 2026

View reviewed changes

modules/local/compute_gene_scores/main.nf Outdated Show resolved Hide resolved

atrigila reviewed Jan 29, 2026

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

apeltzer added 2 commits January 30, 2026 10:03

Address review comments

06faef2

Adding in https URL

9ff740e

apeltzer marked this pull request as ready for review January 30, 2026 10:20

apeltzer added 2 commits January 30, 2026 10:26

Fixing the right containers

911dbd5

Should be fixed entirely now

dac9186

apeltzer added 6 commits January 30, 2026 10:48

Fix test snaps

7d9113a

Merge pull request #161 from nf-core/address-review-comments

2204c77

Address review comments

Update snapshots

ce01141

Wrong docker URI

4d56272

Fix more tests

e4db43a

Merge pull request #162 from nf-core/update-tests

75e362d

Update snapshots

apeltzer approved these changes Jan 30, 2026

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

apeltzer and others added 2 commits January 30, 2026 13:54

Update CHANGELOG.md

190c2cb

Update snapshots

a8dbc29

Merge pull request #164 from delfiterradas/snaps

00102db

Update snapshots

atrigila approved these changes Jan 30, 2026

View reviewed changes

delfiterradas merged commit 6f0b2d5 into master Jan 30, 2026
101 of 103 checks passed

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Make release#158

Make release#158
delfiterradas merged 39 commits intomasterfrom
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delfiterradas commented Jan 29, 2026

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❔ Tests ignored:

✅ Tests passed:

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delfiterradas commented Jan 29, 2026

PR checklist

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nf-core pipelines lint overall result: Passed ✅

❔ Tests ignored:

✅ Tests passed:

Run details

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apeltzer commented Jan 30, 2026

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delfiterradas commented Jan 30, 2026

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github-actions bot commented Jan 29, 2026 •

edited

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