Missing data files in human_bonemarrow (bmmc-reference)

[JohnMCMa]

Hi,

I attempted to recreate the bmmc-reference, and I noticed the current repo did not contain the following files, nor code that generates these files:

• data/hca/manifest.tsv, which I take it to be the HCA manifest file. Can you confirm?
• data/annotations.csv.gz: The snakemake file is the only place this file was mentioned, and nowhere else on this repo. What exactly does this file contain, and how is it generated?

I would appreciate it if you can clarify these issues.

[victor-ramos]

I got the same error as @JohnMCMa

If you upload these files, it would be very much appreciated.

[kandabarau]

I got the same error as @JohnMCMa

If you upload these files, it would be very much appreciated.

since scripts/strip_loom_manifest.sh AWKs some tsv that has to have "bone marrow" in column 35 and "loom" in column 8 - it seems to fit the file one can get from https://explore.data.humancellatlas.org/export/download-manifest selecting Homo Sapiens as Species and loom as File Type
Just save it under data/hca/manifest.tsv and have fun with further errors )