[Do not merge!] Pseudo PR for first release by mashehu · Pull Request #31 · nf-core/lsmquant

mashehu · 2025-10-28T15:23:26Z

Do not merge! This is a PR of dev compared to the TEMPLATE branch for whole-pipeline reviewing purposes. Changes should be made to dev and this PR should not be merged!

integrate divergent branches

…+ meta map

Dev preprocessing

restructuring parameter description

update workflow to take zip archives or directories as input

update Docs + metromap

FriederikeHanssen · 2026-01-20T15:25:24Z

@CaroAMN can you resolve the merge conflicts so the tests can run. Will try to find you some reviewers this week

mashehu · 2026-01-20T15:29:39Z

merge conflict would get resolved by merging the template updates, I guess

CaroAMN · 2026-01-20T16:30:56Z

Hey thank you ! Next week is also fine, i have some updates that i want to include

mashehu · 2026-01-21T09:21:16Z

great, ping me once you have them in

Adding new Subworkflow: numorph_stitch

Merging template updates

github-actions · 2026-02-04T11:21:03Z

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

Posted for pipeline commit de18eb7

+| ✅ 209 tests passed       |+
#| ❔   1 tests had warnings |#
!| ❗  14 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 nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
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!
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
schema_lint - Input mimetype is missing or empty

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ 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-lsmquant_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-lsmquant_logo_light.png
files_exist - File found: docs/images/nf-core-lsmquant_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-lsmquant_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/WorkflowLsmquant.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.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/lsmquant/
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/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/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/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-lsmquant_logo_light.png matches the template
files_unchanged - docs/images/nf-core-lsmquant_logo_light.png matches the template
files_unchanged - docs/images/nf-core-lsmquant_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: 25.04.0, 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_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-gpu.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.
base_config - NUMORPHINTENSITY found in conf/base.config and Nextflow scripts.
base_config - NUMORPHALIGN found in conf/base.config and Nextflow scripts.
base_config - NUMORPHSTITCH found in conf/base.config and Nextflow scripts.
modules_config - conf/modules.config found and not ignored.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - STAGEFILES found in conf/modules.config and Nextflow scripts.
modules_config - NUMORPHINTENSITY found in conf/modules.config and Nextflow scripts.
modules_config - NUMORPHALIGN found in conf/modules.config and Nextflow scripts.
modules_config - NUMORPHSTITCH found in conf/modules.config and Nextflow scripts.
modules_config - NUMORPHRESAMPLE found in conf/modules.config and Nextflow scripts.
modules_config - NUMORPHREGISTER found in conf/modules.config and Nextflow scripts.
modules_config - NUMORPH3DUNET 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 description matches the README.md.

Run details

nf-core/tools version 3.5.1
Run at 2026-02-04 11:20:53

CaroAMN and others added 30 commits June 3, 2024 10:12

started building modules local, started on subworkflows

f4542b5

testing docker container

df4793e

add intensity module

8304298

module:intensity, input/output fix

972c897

testing

cadfd96

testing

84bc7bd

added second module align

881dd10

added third module stitching

abc5470

update readme, added 2 local modules resample + register

5fc80d6

update readme, added metromap

0e1e94e

update

c20148f

update

fa7aaa3

update metromap, adding resampling module

d26aeca

preprocessing basic workflow implementation

cb2c23b

clean up

b062bd7

Update README.md

9ea1737

resample module added

aeb564e

update readme

f28b7c0

Merge pull request #4 from qbic-pipelines/tmp

00f5a3e

integrate divergent branches

added registration module

46b0eed

update workflow logic, emit statements of modules

36a8e86

update moduel output paths

fcf25ee

update

d5bf6fa

update workflow

fe5a930

removed redundant file parsing

e31da22

added: sample_sheet for processing multiple samples + workflow logic …

c3dea04

…+ meta map

clean up + publishing results per sample

9e25dea

Merge pull request #5 from qbic-pipelines/dev_preprocessing

c4868ed

Dev preprocessing

pulling container from quay.io

ccfa907

numorph preprocessing as subworkflow

a1211ed

CaroAMN added 8 commits January 19, 2026 09:44

Merge pull request #42 from CaroAMN/dev

78bd2d5

restructuring parameter description

update workflow to take zip archives or directories as input

7769b09

Merge pull request #43 from CaroAMN/dev

b07aa48

update workflow to take zip archives or directories as input

update metromap, update contributions

2a04042

update metromap

fa0be5b

update docs

3745412

fix ro-crate

87d1ea2

Merge pull request #44 from CaroAMN/dev

09be465

update Docs + metromap

FriederikeHanssen assigned mashehu Jan 20, 2026

CaroAMN added 2 commits January 20, 2026 17:41

adding new subworkflow: intensity+ stitching ( no alignemnt)

77fcd4c

fix typo

4179362

CaroAMN added 14 commits January 21, 2026 15:41

update docs, parameters,schema

1eaf212

update default param

c6f2ee0

update schema

417fda7

fix ro-crate-metadata

318e04f

fix missing channel + brackets

af6468a

fix tests with new params

6532997

update config

77e3c7a

Merge pull request #45 from CaroAMN/dev

651bbd7

Adding new Subworkflow: numorph_stitch

Merged changes from nf-core template

68c520c

update nextflow config

2ff28a7

update snapshot

b7e06e5

update nextflow version

96b17a8

update nextflow version again

7963748

Merge pull request #46 from CaroAMN/merging-template-updates-351

de18eb7

Merging template updates

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[Do not merge!] Pseudo PR for first release#31

[Do not merge!] Pseudo PR for first release#31
mashehu wants to merge 232 commits intoTEMPLATEfrom
dev

mashehu commented Oct 28, 2025

Uh oh!

FriederikeHanssen commented Jan 20, 2026

Uh oh!

mashehu commented Jan 20, 2026

Uh oh!

CaroAMN commented Jan 20, 2026

Uh oh!

mashehu commented Jan 21, 2026

Uh oh!

github-actions bot commented Feb 4, 2026 •

edited

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❗ Test warnings:

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✅ Tests passed:

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mashehu commented Oct 28, 2025

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FriederikeHanssen commented Jan 20, 2026

Uh oh!

mashehu commented Jan 20, 2026

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CaroAMN commented Jan 20, 2026

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mashehu commented Jan 21, 2026

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github-actions bot commented Feb 4, 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 fixed:

✅ Tests passed:

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github-actions bot commented Feb 4, 2026 •

edited

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