Update README.md

[drpatelh]

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
  • If necessary, also make a PR on the nf-core/clipseq 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).

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a8653ee

+| ✅ 159 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  14 tests had warnings |!

Details

❗ Test warnings:

• conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.2 available
• conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.1.1, 3.3.4 available
• conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=6.0, 8.1.1 available
• conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.5.2, 2.8.1 available
• conda_env_yaml - Conda dep outdated: conda-forge::pigz=2.3.4, 2.6 available
• conda_env_yaml - Conda dep outdated: conda-forge::perl=5.26.2, 5.32.0.1 available
• conda_env_yaml - Conda dep outdated: bioconda::multiqc=1.9, 1.10.1 available
• conda_env_yaml - Conda dep outdated: bioconda::cutadapt=3.0, 3.4 available
• conda_env_yaml - Conda dep outdated: bioconda::star=2.6.1d, 2.7.8a available
• conda_env_yaml - Conda dep outdated: bioconda::samtools=1.11, 1.12 available
• conda_env_yaml - Conda dep outdated: bioconda::bedtools=2.29.2, 2.30.0 available
• conda_env_yaml - Conda dep outdated: bioconda::preseq=2.0.3, 3.1.2 available
• conda_env_yaml - Conda dep outdated: bioconda::paraclu=9, 10 available
• conda_env_yaml - Conda dep outdated: bioconda::meme=5.1.1, 5.3.0 available

❔ Tests ignored:

• files_unchanged - File ignored due to lint config: lib/NfcoreSchema.groovy
• files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ 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-clipseq_logo.png
• files_exist - File found: bin/markdown_to_html.py
• files_exist - File found: docs/images/nf-core-clipseq_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/clipseq:dev
• nextflow_config - Config manifest.version ends in dev: '1.1.0dev'
• 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-clipseq_logo.png matches the template
• files_unchanged - bin/markdown_to_html.py matches the template
• files_unchanged - docs/images/nf-core-clipseq_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 - .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
• 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/clipseq:dev
• actions_ci - CI is pulling the correct docker image: docker pull nfcore/clipseq:dev
• actions_ci - CI is tagging docker image correctly: docker tag nfcore/clipseq:dev nfcore/clipseq:dev
• 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: 20.04.0, Config: 20.04.0
• readme - README had a bioconda badge
• conda_env_yaml - Conda environment name was correct (nf-core-clipseq-1.1.0dev)
• 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: conda-forge::pigz=2.3.4
• conda_env_yaml - Conda dep had pinned version number: conda-forge::perl=5.26.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::fastqc=0.11.9
• conda_env_yaml - Conda package is the latest available: bioconda::fastqc=0.11.9
• conda_env_yaml - Conda dep had pinned version number: bioconda::multiqc=1.9
• conda_env_yaml - Conda dep had pinned version number: bioconda::cutadapt=3.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::bowtie2=2.4.2
• conda_env_yaml - Conda package is the latest available: bioconda::bowtie2=2.4.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::star=2.6.1d
• conda_env_yaml - Conda dep had pinned version number: bioconda::samtools=1.11
• conda_env_yaml - Conda dep had pinned version number: bioconda::umi_tools=1.1.1
• conda_env_yaml - Conda package is the latest available: bioconda::umi_tools=1.1.1
• conda_env_yaml - Conda dep had pinned version number: bioconda::bedtools=2.29.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::subread=2.0.1
• conda_env_yaml - Conda package is the latest available: bioconda::subread=2.0.1
• conda_env_yaml - Conda dep had pinned version number: bioconda::preseq=2.0.3
• conda_env_yaml - Conda dep had pinned version number: bioconda::rseqc=4.0.0
• conda_env_yaml - Conda package is the latest available: bioconda::rseqc=4.0.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::icount=2.0.0
• conda_env_yaml - Conda package is the latest available: bioconda::icount=2.0.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::paraclu=9
• conda_env_yaml - Conda dep had pinned version number: bioconda::pureclip=1.3.1
• conda_env_yaml - Conda package is the latest available: bioconda::pureclip=1.3.1
• conda_env_yaml - Conda dep had pinned version number: bioconda::piranha=1.2.1
• conda_env_yaml - Conda package is the latest available: bioconda::piranha=1.2.1
• conda_env_yaml - Conda dep had pinned version number: bioconda::meme=5.1.1
• 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 (55 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_comment.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• merge_markers - No merge markers found in pipeline files

Run details

• nf-core/tools version 1.13.3
• Run at 2021-04-27 11:20:53

[github-actions]

YAML linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

• Install yaml-lint
  • Install npm then install yaml-lint (npm install -g yaml-lint)
• Fix the markdown errors
  • Run the test locally: yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")
  • Fix any reported errors in your YAML files

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

[github-actions]

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

• Install markdownlint-cli
  • On Mac: brew install markdownlint-cli
  • Everything else: Install npm then install markdownlint-cli (npm install -g markdownlint-cli)
• Fix the markdown errors
  • Automatically: markdownlint . --config .github/markdownlint.yml --fix
  • Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!