I have used the fasterq-dump tool over a collection of input files (each input file has a list of accessions to download) to retrieve some data from NCBI SRA. The output is a list of lists of pairs. I would like to convert this into a flat list, i.e. simply a list of pairs. How can I do this?
If that is true, then, most likely, the download failed for some datasets. Try Filter failed on the collection and see if the result becomes selectable by the other tools.
The Apply Rule To Collection and Flatten tools have no obvious limit to their inputs, but also do not seem to offer nested collections as inputs. Perhaps this is a bug.
This is not what I’m observing. All three tools work just fine for me on nested lists.
Can you maybe share an example history with a problematic collection?
Hmm, there seems to be something wrong with these nested collections.
At least in my copy of your shared history there just don’t seem to be any datasets inside of them. Also the dump logs are all empty. If that’s the same for you, it might explain your downstream problems.
I tried again with a smaller set of data, simply this list:
SRR11810704
SRR11810705
and used the Download and Extract Reads in FASTA/Q tool. The output is an empty list, which is surprising. The output should be a list of 2 fastq datasets (this is single ended data).
As a workaround, you should be able to use v 2.10.7+galaxy0 for now.
I think the +galaxy1 version only introduced support an sra_manifest.tabular datatype and the bug