Make validation of ontology terms optional

[wfondrie]

This PR is our hotfix to address #385 by adding the validate_ontologies parameter. When false the SAMPLESHEET_CHECK process will only parse the SDRF file, but will not perform validation.

I'm sure there is a more elegant solution, but I thought this might be helpful as a starting point. Please feel free to ignore if it doesn't go in the right direction.

I'm also happy to add a test if someone could point me in the right direction 😉.

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!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/quantms branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d609e56

+| ✅ 292 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

Details

❗ Test warnings:

• nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

• files_exist - File is ignored: conf/igenomes.config
• files_exist - File is ignored: conf/test_full.config
• files_exist - File is ignored: conf/test.config
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ 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-quantms_logo_light.png
• files_exist - File found: conf/modules.config
• files_exist - File found: docs/images/nf-core-quantms_logo_light.png
• files_exist - File found: docs/images/nf-core-quantms_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: assets/multiqc_config.yml
• 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 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-quantms_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/WorkflowQuantms.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 - 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: params.validationShowHiddenParams
• nextflow_config - Config variable found: params.validationSchemaIgnoreParams
• 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 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: 1.3.0dev
• 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.outdir= ./results
• nextflow_config - Config default value correct: params.local_input_type= mzML
• nextflow_config - Config default value correct: params.decoy_string= DECOY_
• nextflow_config - Config default value correct: params.decoy_string_position= prefix
• nextflow_config - Config default value correct: params.decoy_method= reverse
• nextflow_config - Config default value correct: params.shuffle_max_attempts= 30
• nextflow_config - Config default value correct: params.shuffle_sequence_identity_threshold= 0.5
• nextflow_config - Config default value correct: params.decoydatabase_debug= 0
• nextflow_config - Config default value correct: params.reindex_mzml= true
• nextflow_config - Config default value correct: params.search_engines= comet
• nextflow_config - Config default value correct: params.sage_processes= 1
• nextflow_config - Config default value correct: params.enzyme= Trypsin
• nextflow_config - Config default value correct: params.num_enzyme_termini= fully
• nextflow_config - Config default value correct: params.allowed_missed_cleavages= 2
• nextflow_config - Config default value correct: params.precursor_mass_tolerance= 5
• nextflow_config - Config default value correct: params.precursor_mass_tolerance_unit= ppm
• nextflow_config - Config default value correct: params.fragment_mass_tolerance= 0.03
• nextflow_config - Config default value correct: params.fragment_mass_tolerance_unit= Da
• nextflow_config - Config default value correct: params.fixed_mods= Carbamidomethyl (C)
• nextflow_config - Config default value correct: params.variable_mods= Oxidation (M)
• nextflow_config - Config default value correct: params.fragment_method= HCD
• nextflow_config - Config default value correct: params.isotope_error_range= 0,1
• nextflow_config - Config default value correct: params.protocol= automatic
• nextflow_config - Config default value correct: params.min_precursor_charge= 2
• nextflow_config - Config default value correct: params.max_precursor_charge= 4
• nextflow_config - Config default value correct: params.min_peptide_length= 6
• nextflow_config - Config default value correct: params.max_peptide_length= 40
• nextflow_config - Config default value correct: params.num_hits= 1
• nextflow_config - Config default value correct: params.max_mods= 3
• nextflow_config - Config default value correct: params.min_peaks= 10
• nextflow_config - Config default value correct: params.db_debug= 0
• nextflow_config - Config default value correct: params.mod_localization= Phospho (S),Phospho (T),Phospho (Y)
• nextflow_config - Config default value correct: params.unmatched_action= warn
• nextflow_config - Config default value correct: params.IL_equivalent= true
• nextflow_config - Config default value correct: params.skip_rescoring= false
• nextflow_config - Config default value correct: params.ms2rescore= false
• nextflow_config - Config default value correct: params.rescore_range= independent_run
• nextflow_config - Config default value correct: params.ms2pip_model= HCD2021
• nextflow_config - Config default value correct: params.feature_generators= deeplc,ms2pip
• nextflow_config - Config default value correct: params.calibration_set_size= 0.15
• nextflow_config - Config default value correct: params.posterior_probabilities= percolator
• nextflow_config - Config default value correct: params.run_fdr_cutoff= 0.1
• nextflow_config - Config default value correct: params.extractpsmfeature_debug= 0
• nextflow_config - Config default value correct: params.idfilter_debug= 0
• nextflow_config - Config default value correct: params.pp_debug= 0
• nextflow_config - Config default value correct: params.idscoreswitcher_debug= 0
• nextflow_config - Config default value correct: params.fdr_level= psm_level_fdrs
• nextflow_config - Config default value correct: params.train_FDR= 0.05
• nextflow_config - Config default value correct: params.test_FDR= 0.05
• nextflow_config - Config default value correct: params.subset_max_train= 300000
• nextflow_config - Config default value correct: params.percolator_debug= 0
• nextflow_config - Config default value correct: params.outlier_handling= none
• nextflow_config - Config default value correct: params.idpep_debug= 0
• nextflow_config - Config default value correct: params.consensusid_algorithm= best
• nextflow_config - Config default value correct: params.consensusid_debug= 0
• nextflow_config - Config default value correct: params.reporter_mass_shift= 0.002
• nextflow_config - Config default value correct: params.min_precursor_intensity= 1.0
• nextflow_config - Config default value correct: params.min_precursor_purity= 0.0
• nextflow_config - Config default value correct: params.min_reporter_intensity= 0.0
• nextflow_config - Config default value correct: params.precursor_isotope_deviation= 10.0
• nextflow_config - Config default value correct: params.isotope_correction= true
• nextflow_config - Config default value correct: params.iso_normalization= false
• nextflow_config - Config default value correct: params.reference_channel= 126
• nextflow_config - Config default value correct: params.iso_debug= 0
• nextflow_config - Config default value correct: params.idmapper_debug= 0
• nextflow_config - Config default value correct: params.protein_inference_method= aggregation
• nextflow_config - Config default value correct: params.protein_score= best
• nextflow_config - Config default value correct: params.use_shared_peptides= true
• nextflow_config - Config default value correct: params.min_peptides_per_protein= 1
• nextflow_config - Config default value correct: params.top_PSMs= 1
• nextflow_config - Config default value correct: params.update_PSM_probabilities= false
• nextflow_config - Config default value correct: params.protein_level_fdr_cutoff= 0.01
• nextflow_config - Config default value correct: params.picked_fdr= true
• nextflow_config - Config default value correct: params.psm_level_fdr_cutoff= 0.01
• nextflow_config - Config default value correct: params.protein_inference_debug= 0
• nextflow_config - Config default value correct: params.top= 3
• nextflow_config - Config default value correct: params.average= median
• nextflow_config - Config default value correct: params.ratios= false
• nextflow_config - Config default value correct: params.normalize= false
• nextflow_config - Config default value correct: params.fix_peptides= false
• nextflow_config - Config default value correct: params.include_all= true
• nextflow_config - Config default value correct: params.protein_quant= unique_peptides
• nextflow_config - Config default value correct: params.export_mztab= true
• nextflow_config - Config default value correct: params.protein_quant_debug= 0
• nextflow_config - Config default value correct: params.quantification_method= feature_intensity
• nextflow_config - Config default value correct: params.targeted_only= true
• nextflow_config - Config default value correct: params.feature_with_id_min_score= 0.1
• nextflow_config - Config default value correct: params.feature_without_id_min_score= 0.75
• nextflow_config - Config default value correct: params.lfq_intensity_threshold= 1000.0
• nextflow_config - Config default value correct: params.alignment_order= star
• nextflow_config - Config default value correct: params.quantify_decoys= false
• nextflow_config - Config default value correct: params.plfq_debug= 0
• nextflow_config - Config default value correct: params.mass_acc_automatic= true
• nextflow_config - Config default value correct: params.scan_window_automatic= true
• nextflow_config - Config default value correct: params.scan_window= 8
• nextflow_config - Config default value correct: params.min_corr= 2.0
• nextflow_config - Config default value correct: params.corr_diff= 1.0
• nextflow_config - Config default value correct: params.time_corr_only= true
• nextflow_config - Config default value correct: params.pg_level= 2.0
• nextflow_config - Config default value correct: params.species_genes= false
• nextflow_config - Config default value correct: params.skip_preliminary_analysis= false
• nextflow_config - Config default value correct: params.diann_debug= 3
• nextflow_config - Config default value correct: params.diann_normalize= true
• nextflow_config - Config default value correct: params.random_preanalysis= false
• nextflow_config - Config default value correct: params.empirical_assembly_ms_n= 200
• nextflow_config - Config default value correct: params.msstats_threshold= 0.05
• nextflow_config - Config default value correct: params.add_triqler_output= false
• nextflow_config - Config default value correct: params.msstatslfq_feature_subset_protein= top3
• nextflow_config - Config default value correct: params.msstatslfq_quant_summary_method= TMP
• nextflow_config - Config default value correct: params.msstats_remove_one_feat_prot= true
• nextflow_config - Config default value correct: params.msstatslfq_removeFewMeasurements= true
• nextflow_config - Config default value correct: params.msstatsiso_useunique_peptide= true
• nextflow_config - Config default value correct: params.msstatsiso_rmpsm_withfewmea_withinrun= true
• nextflow_config - Config default value correct: params.msstatsiso_summaryformultiple_psm= sum
• nextflow_config - Config default value correct: params.msstatsiso_summarization_method= msstats
• nextflow_config - Config default value correct: params.msstatsiso_global_norm= true
• nextflow_config - Config default value correct: params.msstatsiso_remove_norm_channel= true
• nextflow_config - Config default value correct: params.msstatsiso_reference_normalization= true
• nextflow_config - Config default value correct: params.msstats_plot_profile_qc= 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.max_cpus= 16
• nextflow_config - Config default value correct: params.max_memory= 128 GB
• nextflow_config - Config default value correct: params.max_time= 10d
• 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.skip_table_plots= false
• nextflow_config - Config default value correct: params.validate_params= true
• 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/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_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 - assets/nf-core-quantms_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-quantms_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-quantms_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_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.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: 23.04.0, Config: 23.04.0
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_todos - No TODO strings found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (225 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/tsv'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: linting.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: ci.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: 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'
• base_config - conf/base.config found and not ignored.
• base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - NFCORE_QUANTMS found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_QUANTMS found in conf/modules.config and Nextflow scripts.
• modules_config - MS2RESCORE found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline

Run details

• nf-core/tools version 2.14.1
• Run at 2024-07-13 07:43:04