PR for 1.1.0 release

[apeltzer]

Many thanks to contributing to nf-core/scrnaseq!

Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested on pull requests (PRs).

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 necessary, also make a PR on the nf-core/scrnaseq branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: https://github.com/nf-core/scrnaseq/tree/master/.github/CONTRIBUTING.md

[apeltzer]

Yeah the failing nf-core lint on release is something that has been fixed in 1.13.3 which is due for release in like 15min? @KevinMenden no?

[ggabernet]

oh noooo another tools release...

[ggabernet]

It would be great to find real sized test data, but I guess we can also leave it for the DSL2 release if we just wanna get this code out now

[ggabernet]

All looks good to me, except there is still the documentation on the parameters that it's not needed any more, and should be removed as it is parsed from the json file now

[apeltzer]

@sk-sahu you want to remove the parameter docs then?

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1156161

+| ✅ 153 tests passed       |+
!| ❗  21 tests had warnings |!

❗ Test warnings:

• 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
• conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.2 available
• conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.1.1, 3.3.4 available
• conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=6.0, 8.1.1 available
• conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.5.2, 2.8.1 available
• conda_env_yaml - Conda dep outdated: bioconda::multiqc=1.8, 1.10 available
• conda_env_yaml - Conda dep outdated: bioconda::bioconductor-isee=1.6.0, 2.2.0 available
• conda_env_yaml - Conda dep outdated: bioconda::bioconductor-tximeta=1.4.0, 1.8.0 available
• conda_env_yaml - Conda dep outdated: bioconda::bioconductor-alevinqc=1.2.0, 1.6.0 available
• conda_env_yaml - Conda dep outdated: bioconda::bioconductor-tximport=1.14.0, 1.18.0 available
• conda_env_yaml - Conda dep outdated: bioconda::star=2.7.2c, 2.7.8a available
• conda_env_yaml - Conda dep outdated: samtools=1.10, 1.12 available
• conda_env_yaml - Conda dep outdated: gffread=0.11.7, 0.12.1 available
• 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
• pipeline_todos - TODO string in awstest.yml: You can customise CI pipeline run tests as required

✅ 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: environment.yml
• files_exist - File found: Dockerfile
• 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
• readme - README had a bioconda badge
• conda_env_yaml - Conda environment name was correct (nf-core-scrnaseq-1.1.0)
• conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.7.3
• conda_env_yaml - Conda dep had pinned version number: conda-forge::markdown=3.1.1
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=6.0
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pygments=2.5.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::multiqc=1.8
• conda_env_yaml - Conda dep had pinned version number: bioconda::salmon=1.4.0
• conda_env_yaml - Conda package is the latest available: bioconda::salmon=1.4.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::r-seurat=3.0.2
• conda_env_yaml - Conda package is the latest available: bioconda::r-seurat=3.0.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::bioconductor-isee=1.6.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::bioconductor-tximeta=1.4.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::bioawk=1.0
• conda_env_yaml - Conda package is the latest available: bioconda::bioawk=1.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::bioconductor-alevinqc=1.2.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::bioconductor-tximport=1.14.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::star=2.7.2c
• conda_env_yaml - Conda dep had pinned version number: samtools=1.10
• conda_env_yaml - Conda dep had pinned version number: gffread=0.11.7
• conda_env_yaml - Conda dep had pinned version number: bioconda::kallisto=0.46.2
• conda_env_yaml - Conda package is the latest available: bioconda::kallisto=0.46.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::bustools=0.40.0
• conda_env_yaml - Conda package is the latest available: bioconda::bustools=0.40.0
• conda_env_yaml - Conda dep had pinned version number: font-ttf-source-code-pro=2.030
• conda_env_yaml - Conda package is the latest available: font-ttf-source-code-pro=2.030
• conda_dockerfile - Found all expected strings in Dockerfile file
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (56 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: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• merge_markers - No merge markers found in pipeline files

Run details

• nf-core/tools version 1.13.3
• Run at 2021-03-26 14:05:59