Refactor for release 2.6

[jonasscheid]

This PR comprises major restructuring to exploit the nextflow groupKey functionality. This change streamlines group-wise processing. Previously, nextflow waited until all processes of a module are done. Now, a downstream process is started once all files of a group have been processed upstream.

group_count and spectra (a key-pair that parses the spectrum filename) are now in the meta map to account for ordered grouping and splitting, especially in the quantification subworkflow. Re-evaluating the quant performance of a spike-in dataset showed that the quantification performance is equally good.

Pre PR	This PR

Furthermore, 7 local modules were replaced by with nf-core modules. More to come 🚀. See https://github.com/nf-core/mhcquant/issues/296

Lets merge this one before the template merge #307 to circumvent some additional merge conflicts.

PR checklist

• [x] 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).
• [x] 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[bot]]

nf-core lint overall result: Failed :x:

Posted for pipeline commit e7a1938

+| ✅ 191 tests passed       |+
!| ❗   5 tests had warnings |!
-| ❌   8 tests failed       |-

### :x: Test failures: * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: `lib/Utils.groovy` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: `lib/WorkflowMain.groovy` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: `lib/NfcoreTemplate.groovy` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: `lib/WorkflowMhcquant.groovy` * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/workflows/branch.yml` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting_comment.yml` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting.yml` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `pyproject.toml` does not match the template ### :heavy_exclamation_mark: Test warnings: * [pipeline_todos](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/pipeline_todos) - TODO string in `WorkflowMhcquant.groovy`: _Optionally add in-text citation tools to this list._ * [system_exit](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/system_exit) - `System.exit` in WorkflowMhcquant.groovy: _System.exit(1)_ [line 18] * [system_exit](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/system_exit) - `System.exit` in WorkflowMhcquant.groovy: _System.exit(1)_ [line 45] * [system_exit](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/system_exit) - `System.exit` in WorkflowMhcquant.groovy: _System.exit(1)_ [line 51] * [system_exit](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/system_exit) - `System.exit` in WorkflowMain.groovy: _System.exit(1)_ [line 53] ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - 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File not found check: `lib/nfcore_external_java_deps.jar` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `.travis.yml` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.name` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.nextflowVersion` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.description` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.version` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.homePage` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `process.cpus` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `process.memory` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `process.time` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `params.outdir` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `params.input` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `params.validationShowHiddenParams` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `params.validationSchemaIgnoreParams` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.mainScript` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.name` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.enable_conda` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``timeline.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``report.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``trace.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``dag.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``manifest.name`` began with ``nf-core/`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.homePage`` began with https://github.com/nf-core/ * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``dag.file`` ended with ``.html`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.nextflowVersion`` started with >= or !>= * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``manifest.version`` ends in ``dev``: ``2.6.0dev`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_version` is set to `master` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Lines for loading custom profiles found * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - nextflow.config contains configuration profile `test` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.pick_ms_levels= 2 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.run_centroidisation= false * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.peptide_min_length= 8 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.peptide_max_length= 12 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.fragment_mass_tolerance= 0.01 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.precursor_mass_tolerance= 5 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.fragment_bin_offset= 0.0 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.number_mods= 3 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.num_hits= 1 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.digest_mass_range= 800:2500 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.prec_charge= 2:3 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.activation_method= ALL * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.enzyme= unspecific cleavage * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_rt_alignment_shift= 300 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.variable_mods= Oxidation (M) * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.remove_precursor_peak= false * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.spectrum_batch_size= 0 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.annotate_ions= false * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.instrument= high_res * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.fdr_level= peptide_level_fdrs * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.fdr_threshold= 0.01 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.rescoring_engine= percolator * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.feature_generators= deeplc,ms2pip * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.ms2pip_model= Immuno-HCD * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.deeplc_calibration_set_size= 0.15 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.subset_affinity_threshold= 500 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.variant_reference= GRCH38 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.variant_annotation_style= SNPEFF * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.variant_indel_filter= false * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.variant_frameshift_filter= false * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_version= master * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.skip_multiqc= false * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_cpus= 16 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_memory= 128.GB * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_time= 240.h * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.publish_dir_mode= copy * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_multiqc_email_size= 25.MB * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.validate_params= true * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.prettierrc.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `CODE_OF_CONDUCT.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `LICENSE` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/.dockstore.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/CONTRIBUTING.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/bug_report.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/config.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/feature_request.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/PULL_REQUEST_TEMPLATE.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `assets/email_template.html` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `assets/email_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `assets/sendmail_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `assets/nf-core-mhcquant_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `docs/images/nf-core-mhcquant_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `docs/images/nf-core-mhcquant_logo_dark.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `docs/README.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.gitignore` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.prettierignore` matches the template * [actions_ci](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' is triggered on expected events * [actions_ci](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' checks minimum NF version * [actions_awstest](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_awstest) - '.github/workflows/awstest.yml' is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` does not use `-profile test` * [readme](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/readme) - README Nextflow minimum version badge matched config. Badge: `23.04.0`, Config: `23.04.0` * [readme](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/readme) - README Zenodo placeholder was replaced with DOI. * [pipeline_name_conventions](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/pipeline_name_conventions) - Name adheres to nf-core convention * [template_strings](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/template_strings) - Did not find any Jinja template strings (167 files) * [schema_lint](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/schema_lint) - Schema lint passed * [schema_lint](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/schema_lint) - Schema title + description lint passed * [schema_lint](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/schema_lint) - Input mimetype lint passed: 'text/csv' * [schema_params](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/schema_params) - Schema matched params returned from nextflow config * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: branch.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awstest.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: ci.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: clean-up.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: fix-linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awsfulltest.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting_comment.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: download_pipeline.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: release-announcements.yml * [merge_markers](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/merge_markers) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/modules_json) - Only installed modules found in `modules.json` * [multiqc_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/multiqc_config) - 'assets/multiqc_config.yml' contains `report_section_order` * [multiqc_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/multiqc_config) - 'assets/multiqc_config.yml' contains `export_plots` * [multiqc_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/multiqc_config) - 'assets/multiqc_config.yml' contains `report_comment` * [multiqc_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/multiqc_config) - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins. * [multiqc_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/multiqc_config) - 'assets/multiqc_config.yml' contains a matching 'report_comment'. * [multiqc_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/multiqc_config) - 'assets/multiqc_config.yml' contains 'export_plots: true'. * [modules_structure](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/modules_structure) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' ### Run details * nf-core/tools version 2.13 * Run at `2024-02-26 16:29:45`