TSV-ify the download images

[sjspielman]

Closes #238

This PR updates all current download images (not including merged) to reflect that all our metadata files are .tsv, not .csv.

There is one additional change here - the spaceranger report along the way got renamed with a -; it was library_spaceranger_summary.html, now library_spaceranger-summary.html. I didn't notice this in #238, but saw it here when I filed the PR. I think it's a good move with other naming changes. The other consequences of this are we have to update the name in scpca-nf (quick fix), and we'd also have to update the file names in the Portal (I guess we can manually rename in prod and include in handoff). Or, we can revert the image back to an _.

Since the reports include the cell type reports, we should only release these updated images with the cell type release, not anndata. So, I'll cherry pick into the cell type release PR once this goes into development. Also, I would note in that CHANGELOG that the spatial summary report name has been tweaked.

[allyhawkins]

The other consequences of this are we have to update the name in scpca-nf (quick fix), and we'd also have to update the file names in the Portal (I guess we can manually rename in prod and include in handoff). Or, we can revert the image back to an _.

I'm fine with making this name change, but given that we aren't going to include these docs changes until cell type annotation, anything that's already handed off can stay the way it is. I don't want to manually rename since there's like 100 samples of spatial, but I would be fine with including this in the release of scpca-nf with the bug fixes (AlexsLemonade/scpca-nf#669) and re-running that project before we hand off cell typing.

[sjspielman]

but given that we aren't going to include these docs changes until cell type annotation, anything that's already handed off can stay the way it is.

Yes, definitely.

I would be fine with including this in the release of scpca-nf with the bug fixes (AlexsLemonade/scpca-nf#669) and re-running that project before we hand off cell typing.

I'll make an issue in admin that blocks the release.

[allyhawkins]

Before I approve this:

• The text in the spatial section should be updated to reflect the new name (https://github.com/AlexsLemonade/scpca-docs/blob/sjspielman/238-tsv-images/docs/download_files.md#spatial-transcriptomics-libraries).
• We need an issue in scpca-nf to update the filename for the spatial summary and have that issue block the release.
• And then a comment on https://github.com/AlexsLemonade/ScPCA-admin/issues/730 about re-running SCPCP000006 prior to hand-off.

[sjspielman]

• The text in the spatial section should be updated to reflect the new name (https://github.com/AlexsLemonade/scpca-docs/blob/sjspielman/238-tsv-images/docs/download_files.md#spatial-transcriptomics-libraries).
  • 134cd3c
• We need an issue in scpca-nf to update the filename for the spatial summary and have that issue block the release.
  • Update spatial report name scpca-nf#678
• And then a comment on Process projects with known references through cell type annotation ScPCA-admin#730 about re-running SCPCP000006 prior to hand-off.
  • https://github.com/AlexsLemonade/ScPCA-admin/issues/730#issuecomment-1915142886
• SJS: Add to cell type docs CHANGELOG
  • 4aaec07

[allyhawkins]

LGTM, although I don't think changing the file name of the spatial report to have - instead of _ means it should be in the changelog, but I think that's a question for @dvenprasad.

[sjspielman]

but I think that's a question for @dvenprasad.

Stay tuned!

[sjspielman]

Ok, it's a no, so I'll revert that commit!