refactor: move shared functions to ccbr_tools and import them here

[kelly-sovacool]

Changes

Import reusable helper functions from ccbr_tools

Issues

resolves #31

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• Write unit tests for any new features, bug fixes, or other code changes.
• [ ] Update docs if there are any API changes.
• [ ] If a new nextflow process is implemented, define the process container and stub.
• [ ] Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

[kopardev]

is there a tacit dependency here on ccbrpipeliner/7 which will load the latest ccbr_tools which will have the tools needed?

[kelly-sovacool]

is there a tacit dependency here on ccbrpipeliner/7 which will load the latest ccbr_tools which will have the tools needed?

yes, this design means we assume our biowulf users will access the pipeline CLIs by loading ccbrpipeliner/7+

if it is installed via pip (ie if someone wanted to install outside of biowulf), ccbr_tools will also be installed because it's a dependency (https://github.com/CCBR/CCBR_NextflowTemplate/pull/32/files#diff-50c86b7ed8ac2cf95bd48334961bf0530cdc77b5a56f852c5c61b89d735fd711R36)