Json schema improvements

[milenaabernardi]

PR checklist

• This comment contains a description of changes (with reason).
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

Comments

change made to the schema_input.json file
the change that was made to line 9 in "required": ["sample", "design", "fastq_1", "panel"],
specifically, "panel" was added to the aforementioned line

the command to run was also changed, I had problems using Docker, so I changed it to singularity
the specific command was as follows nextflow run main.nf -profile test,singularity --outdir results -stub

[nvnieuwk]

Hi, well done already!! Here are some comments. Can you also check the nextflow_schema.json file?

[johandahlberg]

Hi @milenaabernardi! Thank you so much for the contribution! I was wondering what prompted this suggested change. I just wanted to make sure there were no misunderstanding about the panel vs panel_file thing that I alluded to in my inline comment.

[github-actions]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.1.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[github-actions]

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 2c7aa68

+| ✅ 222 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!
-| ❌   2 tests failed       |-

❌ Test failures:

• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
• files_unchanged - .github/workflows/linting_comment.yml does not match the template

❗ Test warnings:

• files_unchanged - LICENSE does not match the template
• pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
• 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.
• pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!

❔ Tests ignored:

• files_exist - File is ignored: assets/multiqc_config.yml
• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/igenomes_ignored.config
• files_unchanged - File ignored due to lint config: assets/nf-core-pixelator_logo_light.png
• actions_ci - actions_ci
• multiqc_config - multiqc_config

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .editorconfig
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/.dockstore.yml
• files_exist - File found: .github/CONTRIBUTING.md
• files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/branch.yml
• files_exist - File found: .github/workflows/ci.yml
• files_exist - File found: .github/workflows/linting_comment.yml
• files_exist - File found: .github/workflows/linting.yml
• files_exist - File found: assets/email_template.html
• files_exist - File found: assets/email_template.txt
• files_exist - File found: assets/sendmail_template.txt
• files_exist - File found: assets/nf-core-pixelator_logo_light.png
• files_exist - File found: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• files_exist - File found: docs/images/nf-core-pixelator_logo_light.png
• files_exist - File found: docs/images/nf-core-pixelator_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: main.nf
• files_exist - File found: conf/base.config
• files_exist - File found: .github/workflows/awstest.yml
• files_exist - File found: .github/workflows/awsfulltest.yml
• files_exist - File found: modules.json
• files_exist - File found: ro-crate-metadata.json
• files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File not found check: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .nf-core.yaml
• files_exist - File not found check: .yamllint.yml
• files_exist - File not found check: bin/markdown_to_html.r
• files_exist - File not found check: conf/aws.config
• files_exist - File not found check: docs/images/nf-core-pixelator_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/WorkflowPixelator.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: validation.help.enabled
• 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 found: validation.help.beforeText
• nextflow_config - Config variable found: validation.help.afterText
• nextflow_config - Config variable found: validation.help.command
• nextflow_config - Config variable found: validation.summary.beforeText
• nextflow_config - Config variable found: validation.summary.afterText
• 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 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: 1.5.0dev
• nextflow_config - Config params.custom_config_version is set to master
• nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Lines for loading custom profiles found
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.save_amplicon_reads= false
• nextflow_config - Config default value correct: params.trim_front= 0
• nextflow_config - Config default value correct: params.trim_tail= 0
• nextflow_config - Config default value correct: params.max_n_bases= 0
• nextflow_config - Config default value correct: params.avg_qual= 20
• nextflow_config - Config default value correct: params.adapterqc_mismatches= 0.1
• nextflow_config - Config default value correct: params.save_qc_passed_reads= false
• nextflow_config - Config default value correct: params.save_qc_failed_reads= false
• nextflow_config - Config default value correct: params.demux_mismatches= 0.1
• nextflow_config - Config default value correct: params.save_demux_processed_reads= false
• nextflow_config - Config default value correct: params.save_demux_failed_reads= false
• nextflow_config - Config default value correct: params.algorithm= adjacency
• nextflow_config - Config default value correct: params.max_neighbours= 60
• nextflow_config - Config default value correct: params.collapse_mismatches= 2
• nextflow_config - Config default value correct: params.collapse_min_count= 2
• nextflow_config - Config default value correct: params.save_collapsed_reads= false
• nextflow_config - Config default value correct: params.multiplet_recovery= true
• nextflow_config - Config default value correct: params.graph_max_refinement_recursion_depth= 5
• nextflow_config - Config default value correct: params.graph_max_edges_to_split= 5
• nextflow_config - Config default value correct: params.graph_min_count= 2
• nextflow_config - Config default value correct: params.save_edgelist= false
• nextflow_config - Config default value correct: params.dynamic_filter= min
• nextflow_config - Config default value correct: params.aggregate_calling= true
• nextflow_config - Config default value correct: params.save_raw_component_metrics= false
• nextflow_config - Config default value correct: params.save_annotate_dataset= false
• nextflow_config - Config default value correct: params.compute_polarization= true
• nextflow_config - Config default value correct: params.compute_colocalization= true
• nextflow_config - Config default value correct: params.polarization_transformation= log1p
• nextflow_config - Config default value correct: params.polarization_n_permutations= 50
• nextflow_config - Config default value correct: params.polarization_min_marker_count= 5
• nextflow_config - Config default value correct: params.colocalization_transformation= rate-diff
• nextflow_config - Config default value correct: params.colocalization_neighbourhood_size= 1
• nextflow_config - Config default value correct: params.colocalization_n_permutations= 50
• nextflow_config - Config default value correct: params.colocalization_min_region_count= 5
• nextflow_config - Config default value correct: params.colocalization_min_marker_count= 5
• nextflow_config - Config default value correct: params.save_analysis_dataset= false
• nextflow_config - Config default value correct: params.no_node_marker_counts= false
• nextflow_config - Config default value correct: params.layout_algorithm= wpmds_3d
• nextflow_config - Config default value correct: params.save_all= false
• nextflow_config - Config default value correct: params.custom_config_version= master
• nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.validate_params= true
• nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - CODE_OF_CONDUCT.md matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/CONTRIBUTING.md matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/workflows/branch.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/images/nf-core-pixelator_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-pixelator_logo_dark.png matches the template
• files_unchanged - docs/README.md matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• 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: 24.04.2, Config: 24.04.2
• readme - README Zenodo placeholder was replaced with DOI.
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: release-announcments.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: template_version_comment.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - PIXELATOR found in conf/modules.config and Nextflow scripts.
• modules_config - PIXELATOR_LIST_OPTIONS found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
• modules_config - PIXELATOR_COLLECT_METADATA found in conf/modules.config and Nextflow scripts.
• modules_config - PIXELATOR_AMPLICON found in conf/modules.config and Nextflow scripts.
• modules_config - PIXELATOR_QC found in conf/modules.config and Nextflow scripts.
• modules_config - PIXELATOR_DEMUX found in conf/modules.config and Nextflow scripts.
• modules_config - PIXELATOR_COLLAPSE found in conf/modules.config and Nextflow scripts.
• modules_config - PIXELATOR_GRAPH found in conf/modules.config and Nextflow scripts.
• modules_config - PIXELATOR_ANNOTATE found in conf/modules.config and Nextflow scripts.
• modules_config - PIXELATOR_ANALYSIS found in conf/modules.config and Nextflow scripts.
• modules_config - PIXELATOR_LAYOUT found in conf/modules.config and Nextflow scripts.
• modules_config - PIXELATOR_REPORT found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.1.1

Run details

• nf-core/tools version 3.1.1
• Run at 2025-03-26 13:38:19

[nvnieuwk]

Some small comments, but looking very good!