DO NOT MERGE: FIRST RELEASE CORE - COMMUNITY PUBLIC REVIEW by maxulysse · Pull Request #165 · nf-core/seqinspector

maxulysse · 2026-01-15T14:36:42Z

PR checklist

Important! Template update for nf-core/tools v3.4.1

Adding Picard tools for QC metrics

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

Added optional Bwa index parameter to skip bwamem2 index for a faster output

Important! Template update for nf-core/tools v3.5.1

github-actions · 2026-01-15T14:50:34Z

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

Posted for pipeline commit 9df5cfc

+| ✅ 192 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 1.0.0
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline

❔ 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 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.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.sort_bam= true
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: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge 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
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 - 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.

Run details

nf-core/tools version 3.5.2
Run at 2026-02-11 09:46:45

mirpedrol

It is looking good! I left some comments to be fixed, but they are minor :)

CITATIONS.md

README.md

modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff

nextflow.config

subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf

modules/local/rundirparser/resources/usr/bin/parse_illumina.py

Skip RUNDIRPARSER if no rundir information is available

nf-core-bot · 2026-02-09T08:26:22Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

Co-authored-by: Pontus Höjer <pontushojer@gmail.com>

mirpedrol

LGTM! thanks for the fixes :)

maxulysse · 2026-02-12T12:30:35Z

Closed as approved by @mirpedrol

FranBonath and others added 30 commits November 7, 2025 11:10

Merge pull request #133 from nf-core/nf-core-template-merge-3.4.1

ebe23fb

Important! Template update for nf-core/tools v3.4.1

Merge branch 'dev' into bwa_index

aa0ee42

Merge branch 'dev' into picard_tools_dev

1e472c8

fix snapshots

b119692

fix snapshots

d45e427

Merge branch 'dev' into multiqc-index

3352f23

.bai files in the same folder as bam files

17bbc74

update snapshots

ce94600

update modules

b9c09ed

update snapshots once again

8e76c46

patch fastqscreen/fastqscreen

f38e893

Merge pull request #128 from agrima2010/picard_tools_dev

de6821f

Adding Picard tools for QC metrics

Merge branch 'dev' into bwa_index

37706c4

Update CHANGELOG.md

c28635a

solve merge conflicts

205c2e3

removed hasta config and corrected nextflow_schema.json

f281848

nextflow_schema.json

6edf19f

nextflow.config

aff9444

removed channel output of BAM from seqinspector.nf

d9373dd

bwa_index added to nextflow.config

2bc95ba

Update nextflow_schema.json

1fc87a8

Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>

Merge pull request #132 from agrima2010/bwa_index

71287cd

Added optional Bwa index parameter to skip bwamem2 index for a faster output

Merge branch 'dev' into nf-core-template-merge-3.5.1

f3b0108

fix multiqc modules install

3a77ea6

Merge pull request #144 from nf-core/nf-core-template-merge-3.5.1

a45f606

Important! Template update for nf-core/tools v3.5.1

Merge branch 'dev' into run-dirs

de0cdb8

Update rundirparser test and add nextflow config for it

b85608c

Fix #94. Remove outdated TODOs

6e961e8

Add #94 to Changelog

a3ad873

Add #94 to Changelog

ab40404

maxulysse added 9 commits December 12, 2025 18:20

fix prepare_genome tests and snapshots

8a49714

code polish

b39fff7

remove file from snapshot

7d4b433

fix qc_bam subworkflow tests

44889d2

update and improve CHANGELOG

eaf4328

add missing entries

bb585d0

code polish

9371567

fix polish

052b7ea

Merge pull request #164 from nf-core/tests_cleanup

a4ba47c

matrulda added 5 commits January 19, 2026 13:47

Skip RUNDIRPARSER if no rundir information is available

cfd4a8d

Add 167 to changelog

6e56eab

Add test for no rundir information scenario

960728a

Add note about RUNDIRPARSER being skipped when not using rundir

e535dc1

pre-commit fix

749aee2

FriederikeHanssen assigned mirpedrol Jan 21, 2026

mirpedrol reviewed Jan 27, 2026

View reviewed changes

matrulda and others added 2 commits February 6, 2026 13:52

Write warning if rundir is missing for a sample

d080687

Merge pull request #167 from matrulda/issue-166_document_rundir_parser

c4052c6

Skip RUNDIRPARSER if no rundir information is available

Address review comments (#168)

9da961c

Co-authored-by: Pontus Höjer <pontushojer@gmail.com>

maxulysse mentioned this pull request Feb 10, 2026

Release 1.0.0 #170

Merged

11 tasks

maxulysse requested a review from mirpedrol February 10, 2026 15:51

maxulysse added 3 commits February 11, 2026 10:45

prepare release 1.0.0 (#169)

9df5cfc

rescure size from the pipeline tests (#171)

204b44d

fix conda env for rundirparser (#172)

2a59538

mirpedrol approved these changes Feb 12, 2026

View reviewed changes

maxulysse closed this Feb 12, 2026

maxulysse changed the title ~~DO NOT MERGE: FIRST RELEASE COMMUNITY REVIEW~~ DO NOT MERGE: FIRST RELEASE CORE - COMMUNITY PUBLIC REVIEW Feb 24, 2026

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DO NOT MERGE: FIRST RELEASE CORE - COMMUNITY PUBLIC REVIEW#165

DO NOT MERGE: FIRST RELEASE CORE - COMMUNITY PUBLIC REVIEW#165
maxulysse wants to merge 636 commits intoempty_masterfrom
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maxulysse commented Jan 15, 2026

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Jan 15, 2026

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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maxulysse commented Feb 12, 2026

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github-actions bot commented Jan 15, 2026 •

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