Merging template updates 3.4.1

[FloWuenne]

Description

Implementing template updates based on work by @kbestak 3.4.1 to dev.

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9b96e76

+| ✅ 252 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   1 tests had warnings |!

Details

❗ Test warnings:

• pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

• files_exist - File is ignored: conf/igenomes_ignored.config
• files_exist - File is ignored: conf/igenomes.config
• files_unchanged - File ignored due to lint config: assets/nf-core-molkart_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-molkart_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-molkart_logo_dark.png
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ 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-molkart_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-molkart_logo_light.png
• files_exist - File found: docs/images/nf-core-molkart_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: .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-molkart_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/WorkflowMolkart.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: 1.2.0dev
• 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.segmentation_method= mesmer
• nextflow_config - Config default value correct: params.cellpose_diameter= 30
• nextflow_config - Config default value correct: params.cellpose_chan= 0
• nextflow_config - Config default value correct: params.cellpose_pretrained_model= cyto
• nextflow_config - Config default value correct: params.cellpose_flow_threshold= 0.4
• nextflow_config - Config default value correct: params.cellpose_edge_exclude= true
• nextflow_config - Config default value correct: params.cellpose_cellprob_threshold= 0
• nextflow_config - Config default value correct: params.mesmer_image_mpp= 0.138
• nextflow_config - Config default value correct: params.mesmer_compartment= whole-cell
• nextflow_config - Config default value correct: params.stardist_model= 2D_versatile_fluo
• nextflow_config - Config default value correct: params.stardist_n_tiles_x= 3
• nextflow_config - Config default value correct: params.stardist_n_tiles_y= 3
• nextflow_config - Config default value correct: params.mindagap_boxsize= 3
• nextflow_config - Config default value correct: params.mindagap_loopnum= 40
• nextflow_config - Config default value correct: params.clahe_cliplimit= 0.01
• nextflow_config - Config default value correct: params.clahe_nbins= 256
• nextflow_config - Config default value correct: params.clahe_pixel_size= 0.138
• nextflow_config - Config default value correct: params.clahe_kernel= 25.0
• nextflow_config - Config default value correct: params.mindagap_tilesize= 2144
• nextflow_config - Config default value correct: params.clahe_pyramid_tile= 1072
• nextflow_config - Config default value correct: params.crop_size_x= 400
• nextflow_config - Config default value correct: params.crop_size_y= 400
• nextflow_config - Config default value correct: params.crop_amount= 4
• nextflow_config - Config default value correct: params.crop_nonzero_fraction= 0.4
• 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/
• nextflow_config - Config default value correct: params.modules_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/
• 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/main.nf.test' contains outdir parameter
• nf_test_content - 'tests/main.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/main.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/main.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/main.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/main.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/main.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/main.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 - docs/README.md 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.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.
• base_config - ILASTIK_PIXELCLASSIFICATION 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 - MOLKARTQC found in conf/modules.config and Nextflow scripts.
• modules_config - MOLKARTQCPNG found in conf/modules.config and Nextflow scripts.
• modules_config - CREATE_STACK found in conf/modules.config and Nextflow scripts.
• modules_config - MASKFILTER found in conf/modules.config and Nextflow scripts.
• modules_config - MINDAGAP_MINDAGAP found in conf/modules.config and Nextflow scripts.
• modules_config - MINDAGAP_DUPLICATEFINDER found in conf/modules.config and Nextflow scripts.
• modules_config - SPOT2CELL found in conf/modules.config and Nextflow scripts.
• modules_config - ILASTIK_PIXELCLASSIFICATION found in conf/modules.config and Nextflow scripts.
• modules_config - ILASTIK_MULTICUT found in conf/modules.config and Nextflow scripts.
• modules_config - CROPHDF5 found in conf/modules.config and Nextflow scripts.
• modules_config - CROPTIFF found in conf/modules.config and Nextflow scripts.
• modules_config - TIFFH5CONVERT found in conf/modules.config and Nextflow scripts.
• modules_config - CLAHE found in conf/modules.config and Nextflow scripts.
• modules_config - STARDIST found in conf/modules.config and Nextflow scripts.
• modules_config - DEEPCELL_MESMER found in conf/modules.config and Nextflow scripts.
• modules_config - CELLPOSE found in conf/modules.config and Nextflow scripts.
• modules_config - CREATE_ANNDATA 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: 3.4.1
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

• nf-core/tools version 3.4.1
• Run at 2025-10-26 14:30:46

[kbestak]

LGTM 🚀
Thank you so much @FloWuenne for ironing out the issues!