Closes #79. This PR adds in the ability to run 5' libraries using the alevin-fry workflow in this repo that we have been using for testing and benchmarking. I chose to keep things fairly simple here and added 10Xv2_5prime to the barcodes and subsequently the tech_list to allow any sample with that technology to be run.
According to https://github.com/COMBINE-lab/salmon/issues/439#issuecomment-547208043, we can modify Alevin-fry to work with 5' libraries by changing the library type from -lISR to -lISF. To do this, I added in a ternary operator that will change the library type only when the 5' libraries are being used. I thought this would be the most straight forward way to do this for testing here, but I'm open to other suggestions on a better way to incorporate this change.
Closes #79. This PR adds in the ability to run 5' libraries using the alevin-fry workflow in this repo that we have been using for testing and benchmarking. I chose to keep things fairly simple here and added
10Xv2_5primeto thebarcodesand subsequently thetech_listto allow any sample with that technology to be run.According to https://github.com/COMBINE-lab/salmon/issues/439#issuecomment-547208043, we can modify Alevin-fry to work with 5' libraries by changing the library type from
-lISRto-lISF. To do this, I added in a ternary operator that will change the library type only when the 5' libraries are being used. I thought this would be the most straight forward way to do this for testing here, but I'm open to other suggestions on a better way to incorporate this change.