Retrieve paths to assets

Once you've assembled a few assets, either by downloading or by building them, you'll be able to use refgenie seek to retrieve the paths. It's quite simple, really -- say you've built the bowtie2_index and fasta assets for hg38. If you type:

refgenie seek -c CONFIG.yaml -g hg38 -a bowtie2_index

You'll get back the absolute path on your system to the bowtie2_index asset, something like:

/path/to/genomes_folder/hg38/bowtie2_index

Because you have also built the fasta asset, you'll have available a few more asset keys to retrieve: fai, fasta, and chrom_sizes. Why is this useful? Instead of writing your shell script to take a path to each the chrom_sizes file and the bowtie2_index path, you just take the genome name, and use refgenie seek to find the correct path. Not only have you simplified the interface to your analysis, but both the script itself and your call of it are now portable.

GENOME="hg38"

refgenie seek -g $GENOME -a bowtie2_index
refgenie seek -g $GENOME -a chrom_sizes
refgenie seek -g $GENOME -a fasta