Add manifest.diagram to nextflow.config

[ewels]

Adds the new manifest.diagram config attribute, pointing at the pipeline overview diagram.

See nf-core/tools#4460 for background: manifest.diagram gives a canonical location for the metro map, so that downstream consumers can find it. We'll use it for the nf-core website soon, for example. The new config option won't be released until Nextflow 26.10, but older versions ignore unknown manifest fields, so it's safe to set in any pipeline today.

[github-actions]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.3.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the Synchronisation documentation.

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d8358cf

+| ✅ 288 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   6 tests had warnings |!

Details

❗ Test warnings:

• files_exist - File not found: conf/igenomes.config
• files_exist - File not found: conf/igenomes_ignored.config
• 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.
• schema_lint - Schema 'description' should be 'A pipeline for spatialomics 10x Xenium In Situ data.'
  Found: 'A pipeline to process spatialomics data from 10x Xenium In Situ or 10x Atera.'
• schema_description - No description provided in schema for parameter: spoqc

❔ 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: .github/workflows/linting_comment.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: assets/nf-core-spatialaxe_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialaxe_logo_light.png
• files_unchanged - File ignored due to lint config: docs/images/nf-core-spatialaxe_logo_dark.png
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

❔ 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/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/pr-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-spatialaxe_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/CONTRIBUTING.md
• files_exist - File found: docs/images/nf-core-spatialaxe_logo_light.png
• files_exist - File found: docs/images/nf-core-spatialaxe_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: 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-spatialaxe_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/WorkflowSpatialaxe.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: 1.0.1dev
• 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.stardist_model= 2D_versatile_fluo
• nextflow_config - Config default value correct: params.stardist_nuclei_model= 2D_versatile_fluo
• nextflow_config - Config default value correct: params.stardist_n_tiles= 8 8
• nextflow_config - Config default value correct: params.run_qc= true
• nextflow_config - Config default value correct: params.cell_segmentation_only= true
• nextflow_config - Config default value correct: params.expansion_distance= 5
• nextflow_config - Config default value correct: params.dapi_filter= 100
• nextflow_config - Config default value correct: params.interior_stain= true
• nextflow_config - Config default value correct: params.boundary_stain= true
• nextflow_config - Config default value correct: params.segger_accelerator= cpu
• nextflow_config - Config default value correct: params.segger_knn_method= kd_tree
• nextflow_config - Config default value correct: params.segger_num_workers= 4
• nextflow_config - Config default value correct: params.format= xenium
• nextflow_config - Config default value correct: params.baysor_scale= 30
• nextflow_config - Config default value correct: params.baysor_tiling= true
• nextflow_config - Config default value correct: params.baysor_tiling_micron= 1200
• nextflow_config - Config default value correct: params.baysor_tiling_overlap= 200
• nextflow_config - Config default value correct: params.baysor_tiling_balanced= true
• nextflow_config - Config default value correct: params.baysor_tiling_scale= 39
• nextflow_config - Config default value correct: params.baysor_tiling_min_mols_per_cell= 120
• nextflow_config - Config default value correct: params.baysor_tiling_min_transcripts_per_cell= 50
• nextflow_config - Config default value correct: params.baysor_prior_confidence= 0.2
• nextflow_config - Config default value correct: params.min_qv= 20.0
• nextflow_config - Config default value correct: params.max_x= 24000.0
• nextflow_config - Config default value correct: params.max_y= 24000.0
• nextflow_config - Config default value correct: params.patch_grid= 3x3
• nextflow_config - Config default value correct: params.patch_overlap= 50
• nextflow_config - Config default value correct: params.patch_filter_iqr_multiplier= 3.0
• nextflow_config - Config default value correct: params.patch_filter_z_threshold= 4.0
• nextflow_config - Config default value correct: params.csplit_x_bins= 2
• nextflow_config - Config default value correct: params.csplit_y_bins= 2
• nextflow_config - Config default value correct: params.tile_width= 120
• nextflow_config - Config default value correct: params.tile_height= 120
• nextflow_config - Config default value correct: params.batch_size_train= 4
• nextflow_config - Config default value correct: params.devices= 4
• nextflow_config - Config default value correct: params.max_epochs= 200
• nextflow_config - Config default value correct: params.batch_size_predict= 1
• nextflow_config - Config default value correct: params.buffer_size= 1
• 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.test_data_base= https://raw.githubusercontent.com/nf-core/test-datasets/spatialaxe
• 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/
• nf_test_content - 'tests/spoqc.nf.test' contains outdir parameter
• nf_test_content - 'tests/spoqc.nf.test' contains outdir parameter
• nf_test_content - 'tests/spoqc.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/spoqc.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/coordinate_mode.nf.test' contains outdir parameter
• nf_test_content - 'tests/coordinate_mode.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/coordinate_mode.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/coordinate_mode.nf.test' contains outdir parameter
• nf_test_content - 'tests/coordinate_mode.nf.test' contains outdir parameter
• nf_test_content - 'tests/coordinate_mode.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/coordinate_mode.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/segfree_mode.nf.test' contains outdir parameter
• nf_test_content - 'tests/segfree_mode.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/segfree_mode.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/preview_mode.nf.test' contains outdir parameter
• nf_test_content - 'tests/preview_mode.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/preview_mode.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/image_mode.nf.test' contains outdir parameter
• nf_test_content - 'tests/image_mode.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/image_mode.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/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/pr-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: 26.04.6, Config: 26.04.6
• 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 - 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: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: pr-comment.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: template-version-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: linting.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
• 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.
• modules_config - conf/modules.config found and not ignored.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC_PRE_XR_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC_POST_XR_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - XENIUMRANGER_RELABEL found in conf/modules.config and Nextflow scripts.
• modules_config - XENIUMRANGER_RESEGMENT found in conf/modules.config and Nextflow scripts.
• modules_config - XENIUMRANGER_IMPORT_SEGMENTATION found in conf/modules.config and Nextflow scripts.
• modules_config - PROSEG found in conf/modules.config and Nextflow scripts.
• modules_config - PROSEG2BAYSOR found in conf/modules.config and Nextflow scripts.
• modules_config - BAYSOR_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - BAYSOR_SEGFREE found in conf/modules.config and Nextflow scripts.
• modules_config - BAYSOR_CREATE_DATASET found in conf/modules.config and Nextflow scripts.
• modules_config - BAYSOR_PREPROCESS_TRANSCRIPTS found in conf/modules.config and Nextflow scripts.
• modules_config - BAYSOR_PREVIEW found in conf/modules.config and Nextflow scripts.
• modules_config - XENIUM_PATCH_DIVIDE found in conf/modules.config and Nextflow scripts.
• modules_config - XENIUM_PATCH_STITCH found in conf/modules.config and Nextflow scripts.
• modules_config - SEGGER_CREATE_DATASET found in conf/modules.config and Nextflow scripts.
• modules_config - SEGGER_TRAIN found in conf/modules.config and Nextflow scripts.
• modules_config - SEGGER_PREDICT found in conf/modules.config and Nextflow scripts.
• modules_config - FICTURE_PREPROCESS found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
• modules_config - RESOLIFT found in conf/modules.config and Nextflow scripts.
• modules_config - PARQUET_TO_CSV found in conf/modules.config and Nextflow scripts.
• modules_config - EXTRACT_PREVIEW_DATA found in conf/modules.config and Nextflow scripts.
• modules_config - GET_TRANSCRIPTS_COORDINATES found in conf/modules.config and Nextflow scripts.
• modules_config - RESIZE_TIF found in conf/modules.config and Nextflow scripts.
• modules_config - SEGGER2XR found in conf/modules.config and Nextflow scripts.
• modules_config - SPLIT_TRANSCRIPTS found in conf/modules.config and Nextflow scripts.
• modules_config - SPATIALDATA_WRITE found in conf/modules.config and Nextflow scripts.
• modules_config - SPATIALDATA_MERGE found in conf/modules.config and Nextflow scripts.
• modules_config - SPATIALDATA_META found in conf/modules.config and Nextflow scripts.
• modules_config - CELLPOSE found in conf/modules.config and Nextflow scripts.
• modules_config - CELLPOSE_CELLS found in conf/modules.config and Nextflow scripts.
• modules_config - STARDIST_NUCLEI found in conf/modules.config and Nextflow scripts.
• modules_config - OPT_FLIP found in conf/modules.config and Nextflow scripts.
• modules_config - OPT_TRACK found in conf/modules.config and Nextflow scripts.
• modules_config - OPT_STAT 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: 4.0.3
• rocrate_readme_sync - RO-Crate description matches the README.md.
• container_configs - conf/containers_conda_lock_files_amd64.config is up to date
• container_configs - conf/containers_conda_lock_files_arm64.config is up to date
• container_configs - conf/containers_docker_amd64.config is up to date
• container_configs - conf/containers_docker_arm64.config is up to date
• container_configs - conf/containers_singularity_https_amd64.config is up to date
• container_configs - conf/containers_singularity_https_arm64.config is up to date
• container_configs - conf/containers_singularity_oras_amd64.config is up to date
• container_configs - conf/containers_singularity_oras_arm64.config is up to date

Run details

• nf-core/tools version 4.0.3
• Run at 2026-09-11 16:11:10

[github-actions]

❌ nf-test failed with latest Nextflow version

Note

Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
Please check if the failure is expected with newer (edge-)releases of Nextflow or if it needs fixing.

• ❌ docker | latest-everything | Shard 8/12

See the full run for details.