Mixcr batch processing I have a folder with 150 pairs of fastq files from an illumina sequence run. I need to precess them with mixcr, how can I do this in a batch with a single command?
Here's how I'd approach this:

for READ1 in /Documents/Data/Input/*R1*
do
    READ2=${READ1/R1/R2}
    mixcr analyze amplicon --s hs \
        --starting-material dna \
        --5-end v-primers \
        --3-end j-primers \
        --adapters no-adapters \
        --receptor-type trb \
        --only-productive "$READ1" "$READ2"
done


Basically, loop over all the R1 FASTQ files in a directory, and calculate the R2 names as needed.

This is using BASH string manipulation, and assumes that substituting R2 for R1 will correctly calculate the R2 filename from R1. It also assumes that all the FASTQ files are in a single directory.