Template Update 3.5.2 & Topics by Tabea01 · Pull Request #365 · nf-core/fetchngs

Tabea01 · 2026-04-15T13:21:27Z

Description

Template update to nf-core/tools version 3.5.2
Topic channels for version reporting (replacing versions.yml)
Updated nf-test snapshots for all pipeline tests
Fixed PIPELINE_INITIALISATION test to include missing help, help_full, show_hidden inputs
Fixed default.nf.test samplesheet MD5 to only hash stable columns (sample, fastq_1, fastq_2) instead of all ENA metadata fields

PR checklist

github-actions · 2026-04-15T13:23:12Z

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

Posted for pipeline commit e2649a4

+| ✅ 202 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   2 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: assets/multiqc_config.yml
files_exist - File is ignored: conf/igenomes.config
files_exist - File is ignored: conf/igenomes_ignored.config
files_exist - File is ignored: conf/modules.config
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
files_unchanged - File ignored due to lint config: assets/nf-core-fetchngs_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-fetchngs_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-fetchngs_logo_dark.png
multiqc_config - multiqc_config
modules_config - modules_config

✅ 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-fetchngs_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-fetchngs_logo_light.png
files_exist - File found: docs/images/nf-core-fetchngs_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: conf/base.config
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-fetchngs_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/WorkflowFetchngs.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 ends in dev: 1.13.0dev
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.sample_mapping_fields= experiment_accession,run_accession,sample_accession,experiment_alias,run_alias,sample_alias,experiment_title,sample_title,sample_description
nextflow_config - Config default value correct: params.nf_core_rnaseq_strandedness= auto
nextflow_config - Config default value correct: params.download_method= ftp
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.validate_params= true
nextflow_config - Config default value correct: params.modules_testdata_base_path= s3://ngi-igenomes/testdata/nf-core/modules/
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= s3://ngi-igenomes/testdata/nf-core/pipelines/fetchngs/1.15.0/
nf_test_content - 'tests/sra_nf_core_pipeline_taxprofiler.nf.test' contains outdir parameter
nf_test_content - 'tests/sra_nf_core_pipeline_taxprofiler.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/sra_custom_ena_metadata_fields.nf.test' contains outdir parameter
nf_test_content - 'tests/sra_custom_ena_metadata_fields.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sra_skip_fastq_download.nf.test' contains outdir parameter
nf_test_content - 'tests/sra_skip_fastq_download.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sra_download_method_fastqdl.nf.test' contains outdir parameter
nf_test_content - 'tests/sra_download_method_fastqdl.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sra_nf_core_pipeline_viralrecon.nf.test' contains outdir parameter
nf_test_content - 'tests/sra_nf_core_pipeline_viralrecon.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/main.nf.test' contains outdir parameter
nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sra_download_method_aspera.nf.test' contains outdir parameter
nf_test_content - 'tests/sra_download_method_aspera.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sra_nf_core_pipeline_atacseq.nf.test' contains outdir parameter
nf_test_content - 'tests/sra_nf_core_pipeline_atacseq.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sra_download_method_sratools.nf.test' contains outdir parameter
nf_test_content - 'tests/sra_download_method_sratools.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sra_nf_core_pipeline_rnaseq.nf.test' contains outdir parameter
nf_test_content - 'tests/sra_nf_core_pipeline_rnaseq.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 - .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 - 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: 25.04.0, Config: 25.04.0
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
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_comment.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: cloudtest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.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
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.
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: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.2
Run at 2026-04-28 13:24:05

jonasscheid

Well done! I see @maxulysse was already faster :D

jonasscheid · 2026-04-28T13:51:34Z

 nextflow_workflow {

-    name "Test workflow: sra/main.nf"
+    name "Test workflow: ../workflows/fetchngs.nf"


What is the difference between the main.nf.test and the default.nf.test? We normally have the "default.nf.test" (tests only basic functionality) and then different tests for different settings

jonasscheid · 2026-04-28T13:53:21Z

+    IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+include { paramsSummaryMap       } from 'plugin/nf-schema'


Tabea01 added 12 commits April 2, 2026 15:18

Template merge WIP

1dd199e

Workflow changes WIP

18609bd

Workflow changes WIP

413fc33

Workflow changes prefetch module WIP

88ab2ee

Update tests WIP

0831206

Update nf test WIP

a0ca3ce

Topic Channels Update WIP

ba7006c

Topic Channels Update 2 WIP

3b9231f

Solved error WIP

92bf756

Solved error in tests and updated snapshots

b2f43ac

changed aspera_cli version WIP

e4c3157

changed aspera_cli version 2nd try WIP

db8b466

Tabea01 added 14 commits April 15, 2026 15:29

changed aspera-cli version WIP

7f4d689

Updated nf-core modules WIP

349515b

Corrected errors

ecd52ef

Updated snapshot

07df5e5

Update snapshots

2eb00fe

Added missing input variables

960ee91

Error handling in default.nf.test and update snapshot

8335f72

Remove trailing whitespace

4599220

Fix samplesheet snapshot to use stable columns only

86ab735

Solve Linting error test

00f554d

Fix mkfg quote escaping in sratoolsncbisettings

9d3f056

Updated subworkflows/nf-core/utils_nfschema_plugin

38ff409

Updated module nf-core/custom/stratoolsncbisettings

c54695b

Changed CHANGELOG.md

851d23c

Tabea01 requested a review from maxulysse April 21, 2026 12:55

Tabea01 changed the title ~~Template Update 3.5.2 & Topics WIP~~ Template Update 3.5.2 & Topics Apr 22, 2026

Tabea01 changed the title ~~Template Update 3.5.2 & Topics~~ Template Update 3.5.2 & Topics WIP Apr 22, 2026

solve aspera-cli webrick error

6d3f8f8

Tabea01 changed the title ~~Template Update 3.5.2 & Topics WIP~~ Template Update 3.5.2 & Topics Apr 24, 2026

Merge branch 'dev' into template_v352

e2649a4

maxulysse approved these changes Apr 28, 2026

View reviewed changes

Tabea01 merged commit dc1918f into nf-core:dev Apr 28, 2026
21 checks passed

jonasscheid reviewed Apr 28, 2026

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Template Update 3.5.2 & Topics#365

Template Update 3.5.2 & Topics#365
Tabea01 merged 28 commits intonf-core:devfrom
Tabea01:template_v352

Tabea01 commented Apr 15, 2026 •

edited

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github-actions Bot commented Apr 15, 2026 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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Tabea01 commented Apr 15, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Description

PR checklist

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github-actions Bot commented Apr 15, 2026 • 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:

Run details

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Tabea01 commented Apr 15, 2026 •

edited

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github-actions Bot commented Apr 15, 2026 •

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