[BIG] Adding spoQC to spatialaxe and many other changes by heylf · Pull Request #206 · nf-core/spatialaxe

heylf · 2026-08-07T14:11:32Z

1. Adding spoQC

Added the entire spoQC quality-control subworkflow: subworkflows/local/spoqc/main.nf plus 31 new local modules under modules/local/spoQC/ (ambient, analysis_category, analysis_cluster, analysis_overview, annotation, bubble, cell, cellcycle, combine_masks, doublet, finalreport, general, hqcr_celltype, hqcr_ident, hqpr_bounding_box, hqpr_celltype, hqpr_clustering, hqpr_metrices, hqpr_refinement, hqtr_ac, hqtr_bounding_box, hqtr_celltype, hqtr_clustering, hqtr_metrices, hqtr_qv, hqtr_refinement, marker, model, transcript, void, whole_slide), each with its own main.nf, meta.yml, and nf-test suite (tests/main.nf.test + snapshot).
Wired spoQC into workflows/spatialaxe.nf.
Added bin/spatialdata_write.py support for spoQC's SpatialData output.
New test configs: conf/tests/test_spoqc.config, conf/tests/test_full_spoqc.config

Comment

Note

The tool will be released soon. It comes with proper documentation and spatialaxe will reference this documentation.

2. spatialaxe resource-label rework

conf/base.config: single process_high/process_low-style labels with a combinatorial label system; process_{tiny,low,mid,high,xl}_cpus, _mem, and _time labels, each scaling with task.attempt.

3. nf-schema plugin upgrade (2.5.1 → 2.7.2)

nextflow.config: bumped the plugin version.
subworkflows/nf-core/utils_nfschema_plugin/main.nf: added a cli_typecast input, renamed parametersSchema → parameters_schema across option maps, fixed --help text resolution.
subworkflows/nf-core/utils_nextflow_pipeline/main.nf: rewrote dumpParametersToJSON to use groovy.json.JsonGenerator with converters for Path/Duration/MemoryUnit/VersionNumber, replacing the old JsonOutput/FilesEx approach.
subworkflows/local/utils_nfcore_spatialaxe_pipeline/main.nf: passes the new cli_typecast argument through.
nextflow_schema.json: cleanup — removed redundant "default": false entries, added "default": true for cell_segmentation_only, added numeric defaults for max_x/max_y, normalized float defaults, unicode-escaped µm.
modules.json / ro-crate-metadata.json: regenerated to match.

4. Bigger test-data support

Added nf-core/unzip module usage so the pipeline can unpack the larger test dataset.
Added assets/samplesheet_full.csv, conf/test_full.config

5. Samplesheet redefintion

sample,bundle,image,annotation,stainings: samplesheet allows for two additional optional columns annotation,stainings that are useful for the QC subworkflow.

6. Rework of subworkflow and pipeline for proper `qc` mode

spatialdata_write_meta_merge/main.nf: Change to subworkflow to account for proper qc mode.
Change to bin/spatialdata_write.py: Adding an all mode to set all available features to True, which is important for QC.
Added bin/spatialdata_write.py support for spoQC's SpatialData output.

PR checklist

…other spoQC modules

…in.nf for utils_nfcore_spatialaxe

….test.snap

dev to spoqc branch to avoid merge conflic

…ge subworkloe, change to mainf and spatialaxe.nf

github-actions · 2026-08-07T14:12:26Z

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 · 2026-08-07T14:13:28Z

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

Posted for pipeline commit 14a6a10

+| ✅ 289 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/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/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/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/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: 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: 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 2026-08-07 16:04:16

github-actions · 2026-08-07T14:23:00Z

❌ 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 5/12

See the full run for details.

heylf and others added 30 commits July 23, 2026 15:51

adding spoqc to spatialaxe

5f6b97a

changing spatialdata_wrote.py

40bef22

all tests pass now for spoQC

bab69c8

updating nextflow configs for the analysis modules

3254152

update README

603637d

adding new module of the final report of spoQC and little changes to …

1112d71

…other spoQC modules

change to final_report main.nf and meta.yml

374a9b6

adding unzip to pipeline for a bigger test data set

ac3a289

changes to lots tests for spoqc modules main.nf.test

62ccb66

adding bigger test data samplesheet_full.csv, test_full.config and ma…

c5b9e64

…in.nf for utils_nfcore_spatialaxe

add untzip to spatialaxe.nf

927aa6e

add test config for spoqc subworkflow

5a41ec8

adding spoqc test, change to .nfignore and spoqc.nf.test and spoqc.nf…

f653407

….test.snap

change to snapshot for final_report main.nf.test.snap

7e5f020

Merge branch 'spoqc' into dev

48339a9

Merge pull request #4 from heylf/dev

a6dfffc

dev to spoqc branch to avoid merge conflic

change to ro-create-metadata.json

a933a14

change to nextflow_schmea.json

dcea0c6

apply prettier modules.json

08217a4

changes to modules.json

d1d824a

changes to nextflow_schmea.json

9862dc0

update nextflow schmema to 2.7.2

73d3207

update subworkflow/nf-core/ultis_nextflow_pipeline

7b88bdd

tiny change to modules.config

bb1dba8

simplify for spoqc the modules.config

32ffd20

change to spoqc resources

55d48d9

add combinatorial cpu labels to base.config

0de40f4

add combinatorial cpu labels to spoqc modules

3df9d01

bugfix because of new nf-core schema version

1bc8bf7

remove spatialdata write from spoqc subworkflow, hcange ot main.nf

65ff8f2

heylf added 7 commits August 7, 2026 15:38

allow for qc mode only approach, change to spatialdata_write_meta_erm…

84fbfb6

…ge subworkloe, change to mainf and spatialaxe.nf

add all changes to CHANGELOG.md

bb74a0c

fix in CHANGELOG.md

9236b5f

change to CHANGELOG.md

ccca85e

update to usage.md

dfecd6e

add spoqc to output.md

5b52705

change to module.jon

f9ec855

trim white spaces

6ff22fd

heylf added 5 commits August 7, 2026 16:28

end-of-file-fixer

4a14fc1

end-of-file-fixer

53312b9

update nextflow version

8a131f5

update nextflow version

246d2cd

upating snapshots

14a6a10

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[BIG] Adding spoQC to spatialaxe and many other changes - #206

[BIG] Adding spoQC to spatialaxe and many other changes#206
heylf wants to merge 43 commits into
nf-core:devfrom
heylf:spoqc

heylf commented Aug 7, 2026 •

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github-actions Bot commented Aug 7, 2026 •

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❗ Test warnings:

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heylf commented Aug 7, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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1. Adding spoQC

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2. spatialaxe resource-label rework

3. nf-schema plugin upgrade (2.5.1 → 2.7.2)

4. Bigger test-data support

5. Samplesheet redefintion

6. Rework of subworkflow and pipeline for proper qc mode

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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github-actions Bot commented Aug 7, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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❌ nf-test failed with latest Nextflow version

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heylf commented Aug 7, 2026 •

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6. Rework of subworkflow and pipeline for proper `qc` mode

github-actions Bot commented Aug 7, 2026 •

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

github-actions Bot commented Aug 7, 2026 •

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