Add option to split projects by samples

[froggleston]

Unless I missed a bit of functionality somewhere, when downloading a whole read set via a project/study identifier, can there be a --by-sample toggle to split the run files up by sample? e.g.

<study_accession>/<sample_accession>/<run_accession>.

[nicsilvester]

The problem with this is that runs and analyses can be linked with multiple samples, so you would end up downloading the same run/analysis data multiple times.
Would it help instead to include in the project/study directory, a report of sample-run/analysis accession mappings?

[froggleston]

Hmm, that's true. But for demultiplexed sequencing runs, each run file will be associated with one sample accession?

[nicsilvester]

Provided the experiment has been submitted correctly, yes. I have seen some instances when an experiment has a list of samples and a list of runs, but no direction as to which run goes with which sample, so all runs then get treated as if they pooled samples.

What complicates it further is that a sample can be used in more than one project.

I can add this request in the "to think about" list. If we introduced this functionality, we'd have to handle runs and analyses with multiple samples (which sample accession should have the run folder, and what happens when you have tens or hundreds of samples for a single run) and analyses with no sample (often caused by an extra large sample list, which is supplied as a file with the analysis data). It's not something we would look at adding quickly.

[froggleston]

OK, that's a sensible outcome.