This PR adds a new workflow called scaffold_and_refine_multitaxa which runs scaffold_and_refine on one input sample (contigs + reads) against many reference genomes from different taxa of interest. This is designed to attempt to assemble all taxa of interest for every sample, and will produce partial and empty outputs for all unsuccessful sample x taxon combinations. It is intended for high throughput metagenomic analyses.
This includes a few updates to tasks to make them more resilient to empty fasta inputs/outputs:
This PR adds a new workflow called
scaffold_and_refine_multitaxawhich runs scaffold_and_refine on one input sample (contigs + reads) against many reference genomes from different taxa of interest. This is designed to attempt to assemble all taxa of interest for every sample, and will produce partial and empty outputs for all unsuccessful sample x taxon combinations. It is intended for high throughput metagenomic analyses.This includes a few updates to tasks to make them more resilient to empty fasta inputs/outputs:
scaffoldrun_discordancealignment_metrics