A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
We have a directory structure where our reference fasta folder is in 1 directory, and then we have different directories that contain the index files of that fasta produced by different tools.
To use the --ref and have it not run bwa index, we include a symlink of the fasta in the bwa index folder. But bwa index is still run, because the workflow is following the symlink and not finding the index files.
We have a directory structure where our reference fasta folder is in 1 directory, and then we have different directories that contain the index files of that fasta produced by different tools.
To use the
--refand have it not runbwa index, we include a symlink of the fasta in the bwa index folder. Butbwa indexis still run, because the workflow is following the symlink and not finding the index files.This PR fixes that.