task checklist from Steve-Miwa meeting about template generator

[sformel-usgs]

• check that all packages are installed
• ensure that readme is using UTC time
• filenaming structure is evolving, update as needed
• sampleMetadata, collection to extraction
• accommodate new data type: experimentMetadata, PCR to Sequencing
• decide input endpoint (probably github)
• add code to generate columns from studyMetadata_user and sampleMetadata_user
• some sections are common to both detection_type but aren't being included in both [sample_collection, sample_storage, sample_preparation, quality_assurance, sample_relations, nucleic_acid_extraction, envrionment]
• make alias for 'detection type' i.e. 'qPCR' along with 'Targeted taxon detection`
• transpose orientation of studyMetadata in output, currently vertical, should be horizontal.
• color of requirement level isn't matching actual term values
• output should have (1) project file, with readme, studyMetdata, sampleMetadata, and experimentMetadata [multitaxa only]
• dnaSeqData should have target_gene + libraryID in filename.
• user manually changes 'libraryID' after template generation, can we automate this instead? Library == pooled libraries, so it should be updated to seq_run_id
• order of terms should remain as they are in the template: some people want to see mandatory first, others want to see native order