Open mkuhn opened 5 years ago
Indeed the docs mention readset
as a valid return type but the code linked above disagrees.
From an implementation point of view this will also require specifying how many fastq files are expected fq1
(single-end), fq2
(paired-end) or fq3
(paired + single) since NGLess has to generate up to 3 output paths.
Another point to consider is if the external tool outputs only 1 file but in interleaved format, something we can now also handle.
I've updated documentation for now but leaving this issue open as we will want to implement support for readset
in the future.
We were trying to add a filtering step as an external module (having a read set as input and output). However, only counts and mapped read sets are supported at the moment, everything else throws an exception:
https://github.com/ngless-toolkit/ngless/blob/bd2bed1f5d951f757c82bf4853c66103f91b5b14/NGLess/ExternalModules.hs#L284
We circumvented this by loading the results with
load_mocat_sample
, so we don't have an urgent need to have this added to the source code. But perhaps a note in the documentation on thertype
would be helpful.