Solve merge conflict by heylf · Pull Request #197 · nf-core/spatialaxe

heylf · 2026-07-28T12:21:59Z

Like the title said it tries to solve the merge conflict for #193

Release version 1.0.0

These files conflicted with the patch and were reset wholesale to the nf-core/tools 4.0.3 template version, on the basis that they carry no pipeline-specific content. If this branch had local edits in them, those edits are gone — please review: .github/workflows/branch.yml .github/workflows/template-version-comment.yml

Remove vulnerable PR-comment artifact pattern

github-actions · 2026-07-28T12:22:51Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 4.0.2.
Please update your pipeline to the latest version.

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

github-actions · 2026-07-28T12:23:48Z

`nf-core pipelines lint` overall result: Failed ❌

Posted for pipeline commit e310c12

+| ✅ 282 tests passed       |+
#| ❔   8 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   4 tests had warnings |!
-| ❌   2 tests failed       |-

Details

❌ Test failures:

files_unchanged - .github/workflows/branch.yml does not match the template
files_unchanged - .github/workflows/linting.yml does not match the template

❗ 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
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/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/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/linting_comment.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_todos - No TODO strings found
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - 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_comment.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: 4.0.2
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 4.0.2
Run at 2026-07-28 12:23:29

kubranarci

if you think necessary, add the change into changelog :)

heylf and others added 6 commits June 17, 2026 15:13

Merge pull request nf-core#139 from nf-core/dev

494cf02

Release version 1.0.0

add zenodo doi

0ed4c69

Merge pull request nf-core#196 from nf-core/patch

fad6e07

Remove vulnerable PR-comment artifact pattern

Merge branch 'master' into solve_merge_conflict

581d3a5

Merge branch 'master' into solve_merge_conflict

e310c12

heylf added 2 commits July 28, 2026 14:28

change branch.yml and linting.yml

63c6a25

change branch.yml and linting.yml

7a98a97

heylf requested a review from nf-core-bot July 28, 2026 12:45

kubranarci approved these changes Jul 28, 2026

View reviewed changes

heylf merged commit c4fdc2a into nf-core:dev Jul 28, 2026
8 checks passed

heylf deleted the solve_merge_conflict branch July 28, 2026 15:18

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Uh oh!

Solve merge conflict - #197

Solve merge conflict#197
heylf merged 8 commits into
nf-core:devfrom
heylf:solve_merge_conflict

heylf commented Jul 28, 2026

Uh oh!

github-actions Bot commented Jul 28, 2026

Uh oh!

github-actions Bot commented Jul 28, 2026

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

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heylf commented Jul 28, 2026

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github-actions Bot commented Jul 28, 2026

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github-actions Bot commented Jul 28, 2026

nf-core pipelines lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

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`nf-core pipelines lint` overall result: Failed ❌