DSL2: single-genome indexing

[jfy133]

Adds indexing for when a user supplies a single fasta file for us as a reference.

I will do a separate PR for the input TSV.

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 - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
  • If necessary, also make a PR on the nf-core/eager 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).
• 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).

[jfy133]

@nf-core-bot fix linting

[jfy133]

@nf-core-bot fix linting

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 996d101

+| ✅ 157 tests passed       |+
!| ❗  19 tests had warnings |!

Details

❗ Test warnings:

• pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
• pipeline_todos - TODO string in README.md: Update the example "typical command" below used to run the pipeline
• pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
• pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
• pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
• pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
• pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
• pipeline_todos - TODO string in base.config: Check the defaults for all processes
• pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
• pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
• pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
• pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
• pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
• pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
• pipeline_todos - TODO string in eager.nf: Add all file path parameters for the pipeline to the list below
• pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
• pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
• pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
• pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output

✅ 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: 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-eager_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-eager_logo_light.png
• files_exist - File found: docs/images/nf-core-eager_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: lib/nfcore_external_java_deps.jar
• files_exist - File found: lib/NfcoreSchema.groovy
• files_exist - File found: lib/NfcoreTemplate.groovy
• files_exist - File found: lib/Utils.groovy
• files_exist - File found: lib/WorkflowMain.groovy
• 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: lib/WorkflowEager.groovy
• 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: .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-eager_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: .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.show_hidden_params
• nextflow_config - Config variable found: params.schema_ignore_params
• 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.version
• 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 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: '3.0.0dev'
• 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
• 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-eager_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-eager_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-eager_logo_dark.png matches the template
• files_unchanged - docs/README.md matches the template
• files_unchanged - lib/nfcore_external_java_deps.jar matches the template
• files_unchanged - lib/NfcoreSchema.groovy matches the template
• files_unchanged - lib/NfcoreTemplate.groovy matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• files_unchanged - pyproject.toml 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: 21.10.3, Config: 21.10.3
• readme - README Nextflow minimum version in Quick Start section matched config. README: 21.10.3, Config: 21.10.3
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (91 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
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: branch.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
• 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'

Run details

• nf-core/tools version 2.6
• Run at 2022-10-10 13:47:26

[FriederikeHanssen]

🚀