minor changes to respond to #19

[ypriverol]

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/pgdb 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 137f9e1

+| ✅ 113 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

• pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi.

❔ Tests ignored:

• nextflow_config - nextflow_config

✅ 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-pgdb_logo.png
• files_exist - File found: bin/markdown_to_html.py
• files_exist - File found: docs/images/nf-core-pgdb_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
• 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-pgdb_logo.png matches the template
• files_unchanged - bin/markdown_to_html.py matches the template
• files_unchanged - docs/images/nf-core-pgdb_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/pgdb:1.0.0
• actions_ci - CI is pulling the correct docker image: docker pull nfcore/pgdb:dev
• actions_ci - CI is tagging docker image correctly: docker tag nfcore/pgdb:dev nfcore/pgdb:1.0.0
• 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
• 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-pgdb-1.0.0)
• conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.9.2
• conda_env_yaml - Conda package is the latest available: conda-forge::python=3.9.2
• conda_env_yaml - Conda dep had pinned version number: conda-forge::markdown=3.3.4
• conda_env_yaml - Conda package is the latest available: conda-forge::markdown=3.3.4
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=8.1.1
• conda_env_yaml - Conda package is the latest available: conda-forge::pymdown-extensions=8.1.1
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pygments=2.8.1
• conda_env_yaml - Conda package is the latest available: conda-forge::pygments=2.8.1
• conda_env_yaml - Conda dep had pinned version number: conda-forge::coreutils=8.31
• conda_env_yaml - Conda package is the latest available: conda-forge::coreutils=8.31
• conda_env_yaml - Conda dep had pinned version number: conda-forge::git-lfs=2.13.3
• conda_env_yaml - Conda package is the latest available: conda-forge::git-lfs=2.13.3
• conda_env_yaml - Conda dep had pinned version number: conda-forge::git=2.30.2
• conda_env_yaml - Conda package is the latest available: conda-forge::git=2.30.2
• conda_env_yaml - Conda dep had pinned version number: bioconda::gffread=0.12.1
• conda_env_yaml - Conda package is the latest available: bioconda::gffread=0.12.1
• conda_env_yaml - Conda dep had pinned version number: bioconda::pypgatk=0.0.19
• conda_env_yaml - Conda package is the latest available: bioconda::pypgatk=0.0.19
• 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: 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 2021-04-15 08:00:39