Implementing revision for hotfix 1.0.1

[heylf]

• docs/usage.md: replaced the hardcoded --outdir ./results in 5 example command blocks with a placeholder --outdir <OUTDIR>, so the docs no longer imply a specific default output directory.
• Removed the outdir = 'results' default parameter from 6 test config files:
  • conf/test.config
  • conf/test_full.config
  • conf/tests/test_coordinate_mode.config
  • conf/tests/test_image_mode.config
  • conf/tests/test_preview_mode.config
  • conf/tests/test_segfree_mode.config
• CHANGELOG.md: updated the 1.0.1 release date from 31.07.2026 to 06.08.2026 and added an entry noting the removal of the default outdir='results' from test profiles.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• CHANGELOG.md is updated.

[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 a1def92

+| ✅ 286 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
• nextflow_config - Config manifest.version should end in dev: 1.0.1
• 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.'

❔ 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 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.offtarget_probe_tracking= false
• 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.use_gpu= false
• nextflow_config - Config default value correct: params.cellpose_downscale= false
• 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.filter_transcripts= false
• 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.tiling= false
• 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.cc_analysis= false
• nextflow_config - Config default value correct: params.buffer_samples= false
• 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/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' snapshots a 'versions.yml' file
• nf_test_content - 'tests/coordinate_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/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/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/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/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: 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 - 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: fix_linting.yml
• actions_schema_validation - Workflow validation passed: awstest.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: branch.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: pr-comment.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.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 2026-08-06 13:18:32