updated default databases to null

[mattheww95]

Set default databases to null and removed options in the Schema.

This PR is solely related to removing defaults in setting for IRIDANext so that incorrect defaults are not populated.

[github-actions]

This PR is against the main branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @mattheww95,

It looks like this pull-request is has been made against the phac-nml/mikrokondo main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the phac-nml/mikrokondo dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 29dfc63

+| ✅ 142 tests passed       |+
#| ❔  31 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: 0.1.2
• readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
• schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/mikrokondo/master/nextflow_schema.json
  Found https://raw.githubusercontent.com/phac-nml/mikrokondo/main/nextflow_schema.json

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-mikrokondo_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-mikrokondo_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-mikrokondo_logo_dark.png
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: docs/output.md
• files_exist - File is ignored: docs/README.md
• files_exist - File is ignored: docs/usage.md
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• files_unchanged - File does not exist: CODE_OF_CONDUCT.md
• files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
• files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
• files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
• files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
• files_unchanged - File ignored due to lint config: assets/email_template.html
• files_unchanged - File ignored due to lint config: assets/email_template.txt
• files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
• files_unchanged - File does not exist: assets/nf-core-mikrokondo_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-mikrokondo_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-mikrokondo_logo_dark.png
• files_unchanged - File does not exist: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/mikrokondo/mikrokondo/.github/workflows/awstest.yml
• multiqc_config - multiqc_config

✅ 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: 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/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: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• 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: modules.json
• files_exist - File found: pyproject.toml
• files_exist - File not found check: Singularity
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: .nf-core.yaml
• 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: .github/workflows/push_dockerhub.yml
• 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: docs/images/nf-core-mikrokondo_logo.png
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .yamllint.yml
• 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/Workflow.groovy
• files_exist - File not found check: lib/Utils.groovy
• files_exist - File not found check: lib/WorkflowMain.groovy
• files_exist - File not found check: lib/NfcoreTemplate.groovy
• files_exist - File not found check: lib/WorkflowMikrokondo.groovy
• 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.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• 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 dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• 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.platform= illumina
• nextflow_config - Config default value correct: params.long_read_opt= nanopore
• 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= 2000.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.validate_params= true
• nextflow_config - Config default value correct: params.tracedir= null/pipeline_info
• nextflow_config - Config default value correct: params.stage_in_mode= symlink
• nextflow_config - Config default value correct: params.validationS3PathCheck= true
• nextflow_config - Config default value correct: params.skip_bakta= true
• nextflow_config - Config default value correct: params.skip_ont_header_cleaning= true
• nextflow_config - Config default value correct: params.fp_average_quality= 25
• nextflow_config - Config default value correct: params.fp_cut_tail_mean_quality= 15
• nextflow_config - Config default value correct: params.fp_cut_tail_window_size= 4
• nextflow_config - Config default value correct: params.fp_complexity_threshold= 20
• nextflow_config - Config default value correct: params.fp_qualified_phred= 15
• nextflow_config - Config default value correct: params.fp_unqualified_precent_limit= 40
• nextflow_config - Config default value correct: params.fp_polyg_min_len= 10
• nextflow_config - Config default value correct: params.fp_polyx_min_len= 10
• nextflow_config - Config default value correct: params.fp_illumina_length_min= 35
• nextflow_config - Config default value correct: params.fp_illumina_length_max= 400
• nextflow_config - Config default value correct: params.fp_single_end_length_min= 1000
• nextflow_config - Config default value correct: params.target_depth= 100
• nextflow_config - Config default value correct: params.min_reads= 1000
• nextflow_config - Config default value correct: params.ba_min_conting_length= 200
• nextflow_config - Config default value correct: params.qt_min_contig_length= 1000
• nextflow_config - Config default value correct: params.mh_min_kmer= 10
• nextflow_config - Config default value correct: params.flye_read_type= hq
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
• pipeline_todos - No TODO strings found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (205 files)
• schema_lint - Schema 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: doc.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.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'

Run details

• nf-core/tools version 2.13.1
• Run at 2024-05-02 13:13:46