Use 'dir' type and checkIfExists for Channel.fromPath

[kelly-sovacool]

Changes

• Use nextflow's Channel.fromPath(type: 'dir') to construct a channel consisting of the directory of reference chromosomes for GEM.
  • Also use this same fix for fastq screen to avoid needing to bind mount the database directory.
• Use checkIfExists: true in all Channel.fromPath calls to make sure an error is thrown if expected files don't exist.
  • This revealed why ci: GitHub Actions doesn't run process stubs from alignment onward #71 is happening.
• Don't use $baseDir for paths. It was deprecated in favor of $projectDir.
  • GitHub Actions build workflow now runs all process stubs. Previously it couldn't find some files due to $baseDir.

Issues

• Resolves Error running gem with biowulf slurm executor: genome sequence file not found at directory #78
• Resolves ci: GitHub Actions doesn't run process stubs from alignment onward #71

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. testing framework not yet implemented
• [ ] Update docs if there are any API changes. on hold until before public release
• [ ] 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/