Release 1.0.1 by maxulysse · Pull Request #188 · nf-core/seqinspector

maxulysse · 2026-03-02T12:45:50Z

Waiting on:

megatests in https://cloud.seqera.io/orgs/nf-core/workspaces/AWSmegatests/watch/1IX1mSkk5AgmW4/v2/logs

PR checklist

* update Zenodo * CHANGELOG * update snapshot * back to dev

Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se>

github-actions · 2026-03-02T13:08:25Z

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

Posted for pipeline commit d8cf330

+| ✅ 198 tests passed       |+
#| ❔   8 tests were ignored |#

Details

❔ Tests ignored:

files_exist - File is ignored: tests/default.nf.test
nextflow_config - Config default ignored: params.fastq_screen_references
nf_test_content - nf_test_content
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: assets/nf-core-seqinspector_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-seqinspector_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-seqinspector_logo_dark.png
multiqc_config - multiqc_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-seqinspector_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-seqinspector_logo_light.png
files_exist - File found: docs/images/nf-core-seqinspector_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-seqinspector_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/WorkflowSeqinspector.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: 1.0.1
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_size= 0.0
nextflow_config - Config default value correct: params.sort_bam= true
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.modules_testdata_base_path= s3://ngi-igenomes/testdata/nf-core/modules/
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/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/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 - 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: branch.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting_comment.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.
base_config - BWAMEM2_MEM found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - SEQTK_SAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - SEQFU_STATS found in conf/modules.config and Nextflow scripts.
modules_config - BWAMEM2_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_CREATESEQUENCEDICTIONARY found in conf/modules.config and Nextflow scripts.
modules_config - BWAMEM2_MEM found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_COLLECTMULTIPLEMETRICS found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_COLLECTHSMETRICS found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - RUNDIRPARSER found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC_GLOBAL found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC_PER_TAG 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: 3.5.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 1.0.1, nfcore_yml.version = 1.0.1
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.5.2
Run at 2026-03-02 14:47:16

LouisLeNezet

I'm not sure about the whole multiqc tags modification, but the test seems okay.
I just got a few question before approving it 😉

.github/workflows/awsfulltest.yml

tests/NovaSeq6000.nf.test.snap

CHANGELOG.md

LouisLeNezet

Fine for me !

FranBonath

Changes tested for the desired outcome, approved!

.github/workflows/awsfulltest.yml

maxulysse and others added 8 commits February 24, 2026 14:00

Back to dev (#181)

8ef4844

* update Zenodo * CHANGELOG * update snapshot * back to dev

FIX: Remove diff for bwamem2/mem (#182)

ed5d23c

FIX: tag collision warning (#183)

2b24d68

Co-authored-by: Adrien Coulier <adrien.coulier@medsci.uu.se>

FIX: No fasta provided (#185)

766d9f1

Add a TAG for MultiQC (#184)

21e4a2b

remove slack url report (#186)

fadb358

prepare release 1.0.1 (#187)

98a1159

Merge branch 'master' into dev

6664ca6

LouisLeNezet reviewed Mar 2, 2026

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LouisLeNezet approved these changes Mar 2, 2026

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FranBonath approved these changes Mar 2, 2026

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maxulysse added 2 commits March 2, 2026 14:46

Fix GHA (#189)

3e1a4a8

indentation (#190)

7a1a8b0

maxulysse commented Mar 2, 2026

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maxulysse commented Mar 2, 2026

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maxulysse commented Mar 2, 2026

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d8cf330

maxulysse merged commit 14106c0 into master Mar 2, 2026
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Release 1.0.1#188

Release 1.0.1#188
maxulysse merged 13 commits intomasterfrom
dev

maxulysse commented Mar 2, 2026 •

edited

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edited

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❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Mar 2, 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 ✅

❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Mar 2, 2026 •

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github-actions bot commented Mar 2, 2026 •

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