DSL2 version with working alevin workflow

[KevinMenden]

I have started with the DSL2 version combining the feat-dsl2 and the current dev branch.
Made a new branch now because I'm not sure which features of feat-dsl2 we might want to keep.

The structure is similar to the viralrecon pipeline. Local and nf-core modules are stored in the modules dir.
Similarly, subworkflows are stored in the subworkflows directory.
Finally we have a workflows directories which stores the different pipeline versions. So we would have one workflow for STARsolo, one for kallisto+bustools and one for alevin. Keeping them separated like this makes it easy to work on one of them without changing (or breaking) another workflow.

I've started with the alevin workflow now, which is basically functional and runs through. I will improve this a bit and clean up some scripts further, but made this PR so that we have a structure to work on.

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fa8009f

+| ✅ 124 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  11 tests had warnings |!

❗ Test warnings:

• files_exist - File not found: environment.yml
• files_exist - File not found: Dockerfile
• nextflow_config - Config manifest.version should end in dev: '1.1.0'
• actions_awsfulltest - .github/workflows/awsfulltest.yml should test full datasets, not -profile test
• pipeline_todos - TODO string in README.md: Write a 1-2 sentence summary of what data the pipeline is for and what it does
• pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of default steps of pipeline
• pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
• 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 awstest.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

❔ Tests ignored:

• conda_env_yaml - No environment.yml file found - skipping conda_env_yaml test
• conda_dockerfile - No environment.yml / Dockerfile file found - skipping conda_dockerfile test

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: CHANGELOG.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.md
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File found: .github/markdownlint.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-scrnaseq_logo.png
• files_exist - File found: bin/markdown_to_html.py
• files_exist - File found: docs/images/nf-core-scrnaseq_logo.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: main.nf
• files_exist - File found: conf/base.config
• files_exist - File found: .github/workflows/awstest.yml
• files_exist - File found: .github/workflows/awsfulltest.yml
• files_exist - File not found check: Singularity
• files_exist - File not found check: parameters.settings.json
• 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: .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: 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 found: process.container
• 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 .svg
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config process.container looks correct: nfcore/scrnaseq:1.1.0
• files_unchanged - .gitattributes 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.md matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.md matches the template
• files_unchanged - .github/markdownlint.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-scrnaseq_logo.png matches the template
• files_unchanged - bin/markdown_to_html.py matches the template
• files_unchanged - docs/images/nf-core-scrnaseq_logo.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 - .gitignore matches the template
• files_unchanged - .github/workflows/push_dockerhub_dev.yml matches the template
• files_unchanged - .github/workflows/push_dockerhub_release.yml matches the template
• files_unchanged - assets/multiqc_config.yaml matches the template
• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - CI is building the correct docker image: docker build --no-cache . -t nfcore/scrnaseq:1.1.0
• actions_ci - CI is pulling the correct docker image: docker pull nfcore/scrnaseq:dev
• actions_ci - CI is tagging docker image correctly: docker tag nfcore/scrnaseq:dev nfcore/scrnaseq:1.1.0
• 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
• readme - README Nextflow minimum version badge matched config. Badge: 20.10.0, Config: 20.10.0
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (96 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_params - Schema matched params returned from nextflow config
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
• merge_markers - No merge markers found in pipeline files

Run details

• nf-core/tools version 1.13.3
• Run at 2021-04-19 12:02:17

[KevinMenden]

The STARsolo "pipeline" is now also implemented, as it consists basically of only two processes currently.

However, this is only tested with some 10X data, and STAR can also handle SmartSeq data. So we need some clever handling of all these different technologies...