This PR should fix that (or at least allow testing properly). I went with leaving the library orientation flag alone in the initial step, as that apparently should not matter, but we have to pass the tech along at least one more step, so I modified some inputs and outputs (in the scpca-nf workflow, this is already done).
For now, I went with the rc option for the 5' data, but we might still consider both as we do seem to have at a pretty significant number of forward reads from the previous analysis!
I should say that this change has not been directly tested as of filing this PR; I wanted to get the suggested changes posted before I will have a chance to do any testing. @ally-hawkins, if you have time to work on testing, that would be great!
After helpful comments from @rob-p, I realized that we didn't do our orientation flip for 5' data in the correct place! https://github.com/AlexsLemonade/alsf-scpca/pull/137#issuecomment-920553327
This PR should fix that (or at least allow testing properly). I went with leaving the library orientation flag alone in the initial step, as that apparently should not matter, but we have to pass the tech along at least one more step, so I modified some inputs and outputs (in the scpca-nf workflow, this is already done).
For now, I went with the
rcoption for the 5' data, but we might still considerbothas we do seem to have at a pretty significant number of forward reads from the previous analysis!I should say that this change has not been directly tested as of filing this PR; I wanted to get the suggested changes posted before I will have a chance to do any testing. @ally-hawkins, if you have time to work on testing, that would be great!