Porting cellranger to DSL2

[ggabernet]

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 add test datasets on the test-datasets folder.
• 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).

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 318d522

+| ✅  66 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗  19 tests had warnings |!

❗ Test warnings:

• files_exist - File not found: conf/igenomes.config
• files_exist - File not found: .github/workflows/awstest.yml
• files_exist - File not found: .github/workflows/awsfulltest.yml
• files_exist - File not found: lib/WorkflowQbic-pipelines/cellranger.groovy
• readme - README did not have a Nextflow minimum version badge.
• readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
• 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.
• pipeline_todos - TODO string in check_samplesheet_multi.py: Update the column names for the input samplesheet
• 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 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_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 cellranger_multi.nf: Add all file path parameters for the pipeline to the list below
• pipeline_todos - TODO string in cellranger.nf: Add all file path parameters for the pipeline to the list below
• pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
• pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters
• schema_description - Ungrouped param in schema: multi_features

❔ Tests ignored:

• files_exist - File is ignored: assets/nf-core-qbic-pipelines/cellranger_logo.png
• files_exist - File is ignored: docs/images/nf-core-qbic-pipelines/cellranger_logo.png
• nextflow_config - nextflow_config
• files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.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.md
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.md
• 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-qbic-pipelines/cellranger_logo.png
• files_unchanged - File ignored due to lint config: bin/scrape_software_versions.py
• files_unchanged - File does not exist: docs/images/nf-core-qbic-pipelines/cellranger_logo.png
• files_unchanged - File ignored due to lint config: docs/README.md
• files_unchanged - File ignored due to lint config: .gitignore or foo
• files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml
• actions_ci - actions_ci
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/cellranger/cellranger/.github/workflows/awstest.yml

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .markdownlint.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.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/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: bin/scrape_software_versions.py
• 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/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: modules/local/get_software_versions.nf
• files_exist - File found: main.nf
• files_exist - File found: assets/multiqc_config.yaml
• files_exist - File found: conf/base.config
• files_exist - File found: modules.json
• 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
• files_unchanged - .gitattributes matches the template
• files_unchanged - .markdownlint.yml matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/workflows/linting_comment.yml 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
• template_strings - Did not find any Jinja template strings (86 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: 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

Run details

• nf-core/tools version 2.1
• Run at 2021-09-10 13:21:44