@nhoffman okay I think this branch is functionally complete now, although could be likely improved a bit in terms of how counts files are packed/unpacked. I have not added specific tests to inspect/verify the adaptor trimming, but would note that the params-its.json is run as part of the automated testing, and therefore both the 'with cutadapt_params' and 'without' conditions are currently included.
@nhoffman okay I think this branch is functionally complete now, although could be likely improved a bit in terms of how counts files are packed/unpacked. I have not added specific tests to inspect/verify the adaptor trimming, but would note that the
params-its.jsonis run as part of the automated testing, and therefore both the 'with cutadapt_params' and 'without' conditions are currently included.