Improve implementation of meta_qc_* utils

[anngvu]

Close #204. Reviewers can see example tests and output improvements for some original motivating cases here:

• https://github.com/nf-osi/dcc-site/issues/139#issuecomment-2501677571
• https://github.com/nf-osi/dcc-site/issues/111#issuecomment-2502143842

Typically these functions should be automated in the background when the time comes instead of being manually run. However, to run this manually:

project_id <- "syn1234"
meta_qc_project(project_id)

**Output table is rendered in a markdown report, which can be inserted anywhere that accepts markdown -- such as GitHub issue threads as seen above.

This is essentially done but needs to hang out in the merge queue/blocked until #202 is merged first since it will rely on/need to incorporate the changes in annotation_qc.R made in #202.

[anngvu]

Ready for review (main reviewer @allaway). Others for awareness.

[cconrad8]

@anngvu I tried this project and it says 0 files found for Raw Data (Young) and the subfolders. I'm wondering if there might be some issues with the subfolders since Raw Data (Young) has many subfolders under neath it.

> meta_qc_project("syn21650484")
Datasets found for QC:
Bulk RNA Sequencing Donor RGCs
Raw Data (Young)
(found 3 files for Bulk RNA Sequencing Donor RGCs)
Found synapse_storage_manifest for dataset named 'Bulk RNA Sequencing Donor RGCs' (syn21650485)!
Downloading files: 100%|██████████| 1.57k/1.57k [00:00<00:00, 4.23kB/s, syn63811146]Downloaded syn63811146 to c:\users\cconrad\.synapsecache\747\148846747\synapse_storage_manifest_rnaseqtemplate.csv
Downloading files: 100%|██████████| 1.57k/1.57k [00:00<00:00, 4.19kB/s, syn63811146]Temp manifest files removed for dataset syn21650485
(found 0 files for Raw Data (Young))
Trying instead: Aim 2, Improving cell engraftment with scaffold; Aim 3, Pig RGCs development
(found 0 files for Aim 2, Improving cell engraftment with scaffold)
(found 0 files for Aim 3, Pig RGCs development)

[anngvu]

@cconrad8 Yeah, this is a good example of where the project structure is structured in a way that we do not expect. Usually there is not a Raw Data folder under a Data folder. If we move Aim 2 and Aim 3 folders to directly under Data, it should work; the check was only updated to accommodate an additional grouping level by Aim or Batch folders etc.

[cconrad8]

Ok @anngvu that makes sense!