Question: If I need to run the same 10x pipeline on multiple libraries, is there a way to do it all at once?
Answer: At the moment, it is not possible to instruct 10x pipelines to run parallel across multiple libraries. However, it is possible to use a bash shell loop to process multiple libraries serially, one after another. If you have a text file called ExpID, with 1 experiment name per line, then a while loop like the following might do the trick:
while read -r ExpID; do cellranger count --id=$ExpID_analysis --transcriptome=/home/path/references/refdata-cellranger-mm10-2.1.0 --fastqs=/home/path/single_cell_exp/$ExpID --sample=$ExpID; done < ExpID