Fix decoydatabase creation

[jonasscheid]

This PR fixes #287: Only one decoy database is created if only one fasta is specified in the input

Also: --include_proteins_from_vcf is temporarily deactivated since vcf parsing is not working #248

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.
• [x] CHANGELOG.md is updated.
• [ ] README.md is updated (including new tool citations and authors/contributors).

[github-actions[bot]]

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

Posted for pipeline commit b8db4a3

+| ✅ 162 tests passed       |+
!| ❗   5 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [pipeline_todos](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `WorkflowMhcquant.groovy`: _Optionally add in-text citation tools to this list._ * [system_exit](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/system_exit.html) - `System.exit` in WorkflowMhcquant.groovy: _System.exit(1)_ [line 18] * [system_exit](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/system_exit.html) - `System.exit` in WorkflowMhcquant.groovy: _System.exit(1)_ [line 45] * [system_exit](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/system_exit.html) - `System.exit` in WorkflowMhcquant.groovy: _System.exit(1)_ [line 51] * [system_exit](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/system_exit.html) - `System.exit` in WorkflowMain.groovy: _System.exit(1)_ [line 51] ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `.nf-core.yml` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `.editorconfig` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `.prettierignore` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `.prettierrc.yml` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `CHANGELOG.md` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `CITATIONS.md` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `nextflow_schema.json` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `nextflow.config` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `README.md` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `.github/.dockstore.yml` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `.github/CONTRIBUTING.md` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - 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File found: `assets/email_template.txt` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `assets/sendmail_template.txt` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `assets/nf-core-mhcquant_logo_light.png` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `conf/modules.config` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `conf/test.config` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `conf/test_full.config` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `docs/images/nf-core-mhcquant_logo_light.png` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - File found: `docs/images/nf-core-mhcquant_logo_dark.png` * [files_exist](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_exist.html) - 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Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `process.cpus` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `process.memory` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `process.time` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `params.outdir` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `params.input` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `params.validationShowHiddenParams` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `params.validationSchemaIgnoreParams` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `manifest.mainScript` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.name` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.enable_conda` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config ``timeline.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config ``report.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config ``trace.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config ``dag.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config ``manifest.name`` began with ``nf-core/`` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable ``manifest.homePage`` began with https://github.com/nf-core/ * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config ``dag.file`` ended with ``.html`` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config variable ``manifest.nextflowVersion`` started with >= or !>= * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config ``manifest.version`` ends in ``dev``: ``2.6.0dev`` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config `params.custom_config_version` is set to `master` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master` * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - Lines for loading custom profiles found * [nextflow_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/nextflow_config.html) - nextflow.config contains configuration profile `test` * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `.prettierrc.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `CODE_OF_CONDUCT.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - 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`.github/workflows/branch.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `.github/workflows/linting_comment.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `.github/workflows/linting.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `assets/email_template.html` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `assets/email_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `assets/sendmail_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `assets/nf-core-mhcquant_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `docs/images/nf-core-mhcquant_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `docs/images/nf-core-mhcquant_logo_dark.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `docs/README.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `lib/nfcore_external_java_deps.jar` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `lib/NfcoreTemplate.groovy` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `.gitignore` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `.prettierignore` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/files_unchanged.html) - `pyproject.toml` matches the template * [actions_ci](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_ci.html) - '.github/workflows/ci.yml' is triggered on expected events * [actions_ci](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_ci.html) - '.github/workflows/ci.yml' checks minimum NF version * [actions_awstest](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_awstest.html) - '.github/workflows/awstest.yml' is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` does not use `-profile test` * [readme](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/readme.html) - README Nextflow minimum version badge matched config. Badge: `23.04.0`, Config: `23.04.0` * [readme](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/readme.html) - README Zenodo placeholder was replaced with DOI. * [pipeline_name_conventions](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/pipeline_name_conventions.html) - Name adheres to nf-core convention * [template_strings](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/template_strings.html) - Did not find any Jinja template strings (142 files) * [schema_lint](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/schema_lint.html) - Schema lint passed * [schema_lint](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/schema_lint.html) - Schema title + description lint passed * [schema_lint](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/schema_lint.html) - Input mimetype lint passed: 'text/csv' * [schema_params](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/schema_params.html) - Schema matched params returned from nextflow config * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: clean-up.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: linting_comment.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: fix-linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: branch.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: release-announcements.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: ci.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: awsfulltest.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: awstest.yml * [merge_markers](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/merge_markers.html) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/modules_json.html) - Only installed modules found in `modules.json` * [multiqc_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains `report_section_order` * [multiqc_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains `export_plots` * [multiqc_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains `report_comment` * [multiqc_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins. * [multiqc_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains a matching 'report_comment'. * [multiqc_config](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains 'export_plots: true'. * [modules_structure](https://nf-co.re/tools/docs/2.11.1/pipeline_lint_tests/modules_structure.html) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' ### Run details * nf-core/tools version 2.11.1 * Run at `2024-01-04 13:54:32`