Remove legacy components

[jonasscheid]

This PR gets rid of a bunch of legacy code and related issues with them #245 #248 #278. This involves the subworkflows refine_fdr, include_proteins, predict_class1 and predict_class2 with all the attached python scripts. The HLA prediction logic and variant handling will we synced with the nf-core/epitopeprediction pipeline in the future.

Most importantly, the ID workflow and quant workflow is not affected by this PR.

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/mhcquant branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile 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 bb9ff54

+| ✅ 233 tests passed       |+

✅ 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-mhcquant_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-mhcquant_logo_light.png
• files_exist - File found: docs/images/nf-core-mhcquant_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: conf/igenomes.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-mhcquant_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/WorkflowMhcquant.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: 2.6.0dev
• 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.run_centroidisation= false
• nextflow_config - Config default value correct: params.pick_ms_levels= 2
• nextflow_config - Config default value correct: params.filter_mzml= false
• nextflow_config - Config default value correct: params.instrument= high_res
• nextflow_config - Config default value correct: params.enzyme= unspecific cleavage
• nextflow_config - Config default value correct: params.activation_method= ALL
• nextflow_config - Config default value correct: params.precursor_mass_tolerance= 5
• nextflow_config - Config default value correct: params.precursor_error_units= ppm
• nextflow_config - Config default value correct: params.fragment_bin_offset= 0.0
• nextflow_config - Config default value correct: params.fragment_mass_tolerance= 0.01
• nextflow_config - Config default value correct: params.number_mods= 3
• nextflow_config - Config default value correct: params.variable_mods= Oxidation (M)
• nextflow_config - Config default value correct: params.num_hits= 1
• nextflow_config - Config default value correct: params.remove_precursor_peak= false
• nextflow_config - Config default value correct: params.spectrum_batch_size= 0
• nextflow_config - Config default value correct: params.rescoring_engine= percolator
• nextflow_config - Config default value correct: params.feature_generators= deeplc,ms2pip
• nextflow_config - Config default value correct: params.ms2pip_model= Immuno-HCD
• nextflow_config - Config default value correct: params.deeplc_calibration_set_size= 0.15
• nextflow_config - Config default value correct: params.fdr_level= peptide_level_fdrs
• nextflow_config - Config default value correct: params.fdr_threshold= 0.01
• nextflow_config - Config default value correct: params.subset_max_train= 0
• nextflow_config - Config default value correct: params.skip_quantification= true
• nextflow_config - Config default value correct: params.max_rt_alignment_shift= 300
• nextflow_config - Config default value correct: params.quantification_min_prob= 0.0
• nextflow_config - Config default value correct: params.quantification_mz_window= 5.0
• nextflow_config - Config default value correct: params.quantification_rt_window= 0.0
• nextflow_config - Config default value correct: params.quantification_mapping_tolerance= 0.0
• nextflow_config - Config default value correct: params.quantification_peak_width= 60.0
• nextflow_config - Config default value correct: params.quantification_min_peak_width= 0.2
• nextflow_config - Config default value correct: params.peptide_min_length= 8
• nextflow_config - Config default value correct: params.peptide_max_length= 12
• nextflow_config - Config default value correct: params.annotate_ions= 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= 240.h
• 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/
• 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/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 - assets/nf-core-mhcquant_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-mhcquant_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-mhcquant_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 (141 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: awstest.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: linting_comment.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 - TDF2MZML found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - THERMORAWFILEPARSER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_DECOYDATABASE found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_PEAKPICKERHIRES found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_IDMERGER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_IDFILTER_Q_VALUE found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_IDFILTER_QUANT found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_IDRIPPER found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_MHCQUANT found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_MHCQUANT found in conf/modules.config and Nextflow scripts.
• modules_config - TDF2MZML found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_FILEFILTER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_MAPALIGNERIDENTIFICATION found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_MAPRTTRANSFORMERMZML found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_COMETADAPTER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_PEPTIDEINDEXER found in conf/modules.config and Nextflow scripts.
• modules_config - MS2RESCORE found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_PERCOLATORADAPTER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_PSMFEATUREEXTRACTOR found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_MZTABEXPORTER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_FEATUREFINDERIDENTIFICATION found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_FEATURELINKERUNLABELEDKD found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_TEXTEXPORTER found in conf/modules.config and Nextflow scripts.
• modules_config - OPENMS_IDCONFLICTRESOLVER found in conf/modules.config and Nextflow scripts.
• modules_config - PYOPENMS_IONANNOTATOR 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: 2.14.1

Run details

• nf-core/tools version 2.14.1
• Run at 2024-05-12 19:07:11

[marissaDubbelaar]

LGTM