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Currently, conversion functions only take one input / output. Will be critical to allow multiple. Impl is easy, api less so (lots to consider: how the conversions, the js transformer, and the cli should handle all this). Will use this issue to propose a few api changes and then select one.
The text was updated successfully, but these errors were encountered:
what if I need to transform something from two sources into one (into dat) and vice-versa. for example, sequence data(fasta) and base qualities (qual) into the combined format (fastq). some bioinformatic softwares prefer fasta+qual others fastq so you end up using a custom python, perl or other tool to convert, usually using libraries like biopython
So cli should definitely let you do this. Something like
# --flags have to come after pipeline because of ambiguity.
transform <pipeline> [--inputs <inputs>] [--outputs <outputs>]
# or add --pipeline flag for whatever order
transform [--pipeline <pipeline>] [--inputs <inputs>] [--outputs <outputs>]
# or use -- delimiters
transform [<inputs> --] <pipeline> [-- <outputs>]
Does anyone have good examples of clis that take variable number of input + output files?
Currently, conversion functions only take one input / output. Will be critical to allow multiple. Impl is easy, api less so (lots to consider: how the conversions, the js transformer, and the cli should handle all this). Will use this issue to propose a few api changes and then select one.
The text was updated successfully, but these errors were encountered: