Hi Luis,
A minor suggestion: including feature length in the count table.
In a bit more details: `count` function may output the results normalized by the feature lengths: `{raw/normed/scaled}`. From the point of view of the downstream data manipulation, I would prefer to have raw reads that I could normalize by the feature length when necessary. As of now I have to import these lengths from the catalogue and merge them with the count table outside of NGLess.
A less minor disadvantage is the necessity to launch NGLess as many times as there are the samples. Thus, one has to use an external script or a different software for organizing workflow, reducing NGLess to a command line tool. But I suppose this is not counted as "small improvements"
Regards, Vadim.