Notes
Hopefully this handles most of the conditional situations with DSP and project structure*, but there many different situations so possibly I haven't covered everything and would appreciate more testing. This is meant to be run as an automated first-pass to help whoever is doing closeout.
Also the format/how things surfaced is not completely optimized yet (suggest add'l ideas in an enhancement issue, unless they're easy fixes that can go directly into this PR).
It does not* handle a legacy project but will let you know if things fail due to non-standard structure. Report can be run after project cleanup/remediation.
Instructions
Install pkg on this branch
Make a copy of template with rmarkdown::draft("report3", template = "checkpoint-closeout-report", package = "nfportalutils", edit = FALSE)
Update params in Rmd to run a report with some project, with or without a DSP. Example of the output structure:
Developments to support https://github.com/nf-osi/dcc-site/issues/694 and close #145 and #146.
Notes Hopefully this handles most of the conditional situations with DSP and project structure*, but there many different situations so possibly I haven't covered everything and would appreciate more testing. This is meant to be run as an automated first-pass to help whoever is doing closeout.
Also the format/how things surfaced is not completely optimized yet (suggest add'l ideas in an enhancement issue, unless they're easy fixes that can go directly into this PR).
It does not* handle a legacy project but will let you know if things fail due to non-standard structure. Report can be run after project cleanup/remediation.
Instructions
rmarkdown::draft("report3", template = "checkpoint-closeout-report", package = "nfportalutils", edit = FALSE)