Download samples from SRA

[mkatsanto]

Is your feature request related to a problem? Please describe.
Extension for SRA sample download compatibility

Describe the solution you'd like
Implementation in extensions/sra.py

Additional context
Execute only if the user inputs any SRA sample identifiers
Python package for retrieving metadata and downloading datasets from SRA/ENA: https://pypi.org/project/pysradb/

[mkatsanto]

https://git.scicore.unibas.ch/zavolan_group/pipelines/zarp/-/issues/122

[mzavolan]

Tried to install and test the pysradb code. Errors all over the place. I don't think this is usable for the time being.

[mzavolan]

Tried to install and test the pysradb code. Errors all over the place. I don't think this is usable for the time being.

Filed a bug report, the developer is aware of the issue and will try to fix it.

[dominikburri]

As discussed with @uniqueg and @mzavolan, we will write a separate Snakemake workflow for SRA downloads (using fastq-dump), similar to how we run HTSinfer. Will open new issues for that.

[uniqueg]

Just a note that this functionality should consider the --execution-mode. If the value is DRY_RUN, the samples shouldn't actually be downloaded. Instead it should be logged what would be downloaded.