Ideas for various convenience scripts

vicfabienne commented 3 years ago

[ ] initialize the sample sheet from a given list of filenames when filenames follow a certain naming scheme Making those sample sheets can be quite tedious. I think it should be possible to initialize those files from a list of raw-data-fastq files. A very basic version could at least initialize it with the columns for sample name and read1, read2 filled. I can also think of suggesting a certain naming scheme for the filenames in order to parse even more metadata - like location, time points, etc from those filenames. I think it would be very nice when we can make it possible that someone only has to add additional metadata
[x] replace manual database download with a script as suggested by @rekado

rekado commented 3 years ago

These are two very different things. Could you please open a separate issue for each?

rekado commented 3 years ago

I added a download script in f16172100dad0c364e88d86d34be52169a68353f.

vicfabienne commented 3 years ago

Shall I still split it? And some point I was just not sure anymore if I'm not flooding the tracker to much with small things

BIMSBbioinfo / pigx_sars-cov-2