Closes #86. I have updated the previous notebook that was being used to compare time and memory usage across the tools we are using for benchmarking to include 2 new snRNA-seq samples (SCPCR000118, SCPCR000119) and new configurations that we have implemented for alevin-fry. In addition to having alevin-fry in --sketch mode, we have also added in using the --unfiltered-pl flag with or without the --sketch flag.
This PR also includes adding the nextflow trace files for each of the runs that was performed. Each tool now has three associated trace files.
the four scRNA seq samples
the two snRNA seq samples run with the cDNA index
the two snRNA seq samples run with the pre-mRNA index
For file name consistency, I updated the file names of the previously added trace files that were orginally named allsamples.trace.txt so they will also show up in the diff.
In general, snRNA-seq samples result in increased memory and runtime, with the biggest effect on memory usage seen in Kallisto and runtime in Cellranger.
Alevin-fry remains having the lowest memory usage, and using the --sketch parameter reduces the runtime.
Closes #86. I have updated the previous notebook that was being used to compare time and memory usage across the tools we are using for benchmarking to include 2 new snRNA-seq samples (SCPCR000118, SCPCR000119) and new configurations that we have implemented for alevin-fry. In addition to having alevin-fry in
--sketchmode, we have also added in using the--unfiltered-plflag with or without the--sketchflag.This PR also includes adding the nextflow trace files for each of the runs that was performed. Each tool now has three associated trace files.
allsamples.trace.txtso they will also show up in the diff.In general, snRNA-seq samples result in increased memory and runtime, with the biggest effect on memory usage seen in Kallisto and runtime in Cellranger. Alevin-fry remains having the lowest memory usage, and using the
--sketchparameter reduces the runtime.