Apply Hartwig updates, fixes

Open scwatts opened this issue 1 month ago • 2 comments

Nov 28 '25 02:11 scwatts

`nf-core pipelines lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit c0c5aff

+| ✅ 210 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗  17 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

files_exist - File not found: assets/multiqc_config.yml
files_unchanged - LICENSE does not match the template
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
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!
schema_params - Schema param panel not found from nextflow config
schema_params - Schema param fastp_umi_location not found from nextflow config
schema_params - Schema param fastp_umi_length not found from nextflow config
schema_params - Schema param fastp_umi_skip not found from nextflow config
schema_params - Schema param redux_umi_duplex_delim not found from nextflow config
schema_params - Schema param genome_version not found from nextflow config
schema_params - Schema param genome_type not found from nextflow config
schema_params - Schema param ref_data_hmf_data_path not found from nextflow config
schema_params - Schema param ref_data_panel_data_path not found from nextflow config
schema_params - Schema param ref_data_genome_gtf not found from nextflow config
schema_params - Schema param ref_data_hla_slice_bed not found from nextflow config
schema_description - No description provided in schema for parameter: prepare_reference_only

:grey_question: Tests ignored:

files_exist - File is ignored: lib/Utils.groovy
files_exist - File is ignored: lib/WorkflowMain.groovy
files_exist - File is ignored: lib/WorkflowOncoanalyser.groovy
nextflow_config - Config default ignored: params.fastp_umi_length
nextflow_config - Config default ignored: params.fastp_umi_skip
nf_test_content - nf_test_content
files_unchanged - File ignored due to lint config: assets/nf-core-oncoanalyser_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-oncoanalyser_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-oncoanalyser_logo_dark.png
multiqc_config - multiqc_config

:white_check_mark: 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/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/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_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-oncoanalyser_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-oncoanalyser_logo_light.png
files_exist - File found: docs/images/nf-core-oncoanalyser_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: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: conf/igenomes_ignored.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-oncoanalyser_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/Workflow.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: 2.2.0dev
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.force_genome= false
nextflow_config - Config default value correct: params.force_panel= false
nextflow_config - Config default value correct: params.create_stub_placeholders= false
nextflow_config - Config default value correct: params.max_fastq_records= 10000000
nextflow_config - Config default value correct: params.fastp_umi_enabled= false
nextflow_config - Config default value correct: params.redux_umi_enabled= false
nextflow_config - Config default value correct: params.isofox_functions= TRANSCRIPT_COUNTS;ALT_SPLICE_JUNCTIONS;FUSIONS;RETAINED_INTRONS
nextflow_config - Config default value correct: params.hmftools_log_level= DEBUG
nextflow_config - Config default value correct: params.igenomes_ignore= true
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.hmf_genomes_base= https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes
nextflow_config - Config default value correct: params.prepare_reference_only= 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/oncoanalyser
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/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_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
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore 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 - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.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'
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 - WRITE_REFERENCE_DATA found in conf/modules.config and Nextflow scripts.
modules_config - FASTP found in conf/modules.config and Nextflow scripts.
modules_config - STAR_GENOMEGENERATE found in conf/modules.config and Nextflow scripts.
modules_config - GATK4_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
modules_config - REDUX found in conf/modules.config and Nextflow scripts.
modules_config - AMBER found in conf/modules.config and Nextflow scripts.
modules_config - COBALT found in conf/modules.config and Nextflow scripts.
modules_config - PURPLE found in conf/modules.config and Nextflow scripts.
modules_config - CIDER found in conf/modules.config and Nextflow scripts.
modules_config - BAMTOOLS found in conf/modules.config and Nextflow scripts.
modules_config - CHORD found in conf/modules.config and Nextflow scripts.
modules_config - LILAC found in conf/modules.config and Nextflow scripts.
modules_config - SIGS found in conf/modules.config and Nextflow scripts.
modules_config - TEAL found in conf/modules.config and Nextflow scripts.
modules_config - VIRUSBREAKEND found in conf/modules.config and Nextflow scripts.
modules_config - VIRUSINTERPRETER found in conf/modules.config and Nextflow scripts.
modules_config - ISOFOX found in conf/modules.config and Nextflow scripts.
modules_config - NEO_SCORER found in conf/modules.config and Nextflow scripts.
modules_config - NEO_FINDER found in conf/modules.config and Nextflow scripts.
modules_config - WISP found in conf/modules.config and Nextflow scripts.
modules_config - CUPPA found in conf/modules.config and Nextflow scripts.
modules_config - PEACH found in conf/modules.config and Nextflow scripts.
modules_config - ORANGE found in conf/modules.config and Nextflow scripts.
modules_config - COBALT_PANEL_NORMALISATION found in conf/modules.config and Nextflow scripts.
modules_config - PAVE_PON_PANEL_CREATION found in conf/modules.config and Nextflow scripts.
modules_config - ISOFOX_PANEL_NORMALISATION 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: 3.5.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.5.1
Run at 2025-11-28 02:51:03

Nov 28 '25 02:11 github-actions[bot]

Test failures are to be addressed in https://github.com/nf-core/oncoanalyser/pull/265

Nov 28 '25 03:11 scwatts

Apply Hartwig updates, fixes

nf-core pipelines lint overall result: Passed :white_check_mark: :warning:

:heavy_exclamation_mark: Test warnings:

:grey_question: Tests ignored:

:white_check_mark: Tests passed:

Run details

`nf-core pipelines lint` overall result: Passed :white_check_mark: :warning: