One of the changes that came with alevin-fry was a new mapping option in salmon alevin that performs pseudomapping that is much more similar to kallisto. This does make it much faster, so it is an option we might well want to explore in benchmarking (#63). I am here proposing that we make this a workflow option using nextflow params so that we can easily switch between the two for benchmarking.
Note that we will also probably want to add something to the output directory (for publishDir flags) or the work directory currently defined as run_dir so that we do not accidentally clobber previous results.
One of the changes that came with
alevin-frywas a new mapping option insalmon alevinthat performs pseudomapping that is much more similar tokallisto. This does make it much faster, so it is an option we might well want to explore in benchmarking (#63). I am here proposing that we make this a workflow option using nextflowparamsso that we can easily switch between the two for benchmarking.Note that we will also probably want to add something to the output directory (for
publishDirflags) or the work directory currently defined asrun_dirso that we do not accidentally clobber previous results.