> It might seem odd to prefer shell scripting over a full-featured dynamic scripting language, but shell scripts like this have some material advantages over Python:

And thus 99% of bioinformatics pipelines are shell at their heart... You need 10 packages, written in 4 different programming languages, and the common interfaces are files and pipes.

And for that matter, this could use a named pipe rather than a file (assuming `odgi depth` only uses streaming access):

    odgi depth -i chr8.pan.og -r chm13#chr8 | \
        bedtools makewindows -b /dev/stdin -w 5000 > chm13.chr8.w5kbps.bed
    
    odgi depth -i chr8.pan.og -b chm13.chr8.w5kbps.bed --threads 2 | \
        bedtools sort > chr8.pan.depth.w5kbps.bed

And Bash process substitution allows writing it all without an explicitly named pipe, though it may look a bit ugly:

    odgi depth -i chr8.pan.og -b --threads 2 <( \
            odgi depth -i chr8.pan.og -r chm13#chr8 | \
            bedtools makewindows -b /dev/stdin -w 5000
        ) | \
        bedtools sort > chr8.pan.depth.w5kbps.bed

Which is why bioinformaticians get bad reputations with software engineers. (I still have a fair amount of misplaced pride for adding a shebang to a Makefile once to make a pipeline into a command several decades ago...)