Add sample metadata table to QC and cell type reports

[allyhawkins]

Is your feature request related to a problem? Please describe.

See https://github.com/AlexsLemonade/scpca-portal/issues/759

Describe the solution you'd like A clear and concise description of what you want to happen.

We would like to include a sample metadata table in the main QC report. This should be included along with the processing and library tables that are currently present and should include things like:

• sample ID
• diagnosis
• subdiagnosis
• tissue location
• age
• sex
• disease timing

We want to include any sample metadata that is consistently collected across samples.

Additional context

We might consider adding in the ontology IDs here as well. We will also have to make sure we account for things being NA as some samples do have missing information.

[allyhawkins]

Just noting that we should include this same table in both the main and cell type reports.

[jaclyn-taroni]

I changed the title to reflect https://github.com/AlexsLemonade/scpca-nf/issues/765#issuecomment-2176490048.

[allyhawkins]

As I started working on this, there were two things that came up that I think could benefit from asynchronous discussion:

• What fields do we want to include in the table, specifically do we want to include ontology IDs and human readable values?
• How do we want the table to look for multiplexed libraries. We could break up the table into individual sample metadata tables for each sample in the library or create a table with all samples? I think I would favor including all samples in one table, but we should probably consider how it would look for libraries that have 4-6 samples.

Here's an example of what the table would look like with multiple samples for reference:

[allyhawkins]

To summarize our discussion in pre-planning, we will not include ontology IDs, but may include a link to the ontology ID if it's not too big of a lift. For multiplexed samples, we are not going to provide sample information but instead a blue box indicating that no sample metadata is provided because the library has samples that have been multiplexed.

[allyhawkins]

Closed by #769