bripipetools issues overview

[spribitzer]

This is a collection of issues that should be addressed during the next rework of bripipetools:

• [ ] add ATACseq #120 and Cut and Run functions
• [ ] push MiXCR data by project not flowcell #119
• [ ] 10x to research database #118
• [ ] rhapsody to research database (maybe even a general/manual push to database script)
• [ ] partial downloads from base space
• [ ] improve handling of files in globus_batch_submit folder #113
• [ ] avoiding double submissions #114
• [ ] write documentation on how to run flowcells (epigenetic, RNAseq, 10x, rhapsody,...)
• [ ] in general: handle create/delete folders commands more gracefully
• [ ] cleanup /archive workflows, update annotations, and add new ones for ATAC/Cut and Run and update
• [ ] the summarize mixcr script that pushes TCRs to the research database should be able to overwrite existing TCRs, and also use the credentials from the config.ini file
• [ ] update documentation
• [ ] add timestamps to runs and automatically calculate runtimes (per library, project, flowcell) and push to research database
• [ ] can we automate the step where we give people BAP permissions?

[spribitzer]

• [ ] verify integrity of data before wrapping up, e.g. make sure all the metrics are files, and not folder. ideally there would be a list of libraries that are missing something at the end