Merging Charlotte's (@royercj) pre-mycosnp workflow code additions working towards automated reference genome selection and clade assignment. These elements build out new feature functionality based on average nucleotide identity (ANI) computed by the program Sourmash to determine a species classification for new genomes, as well as a clade assignment for C. auris. These new features are part of a workflow pre_mycosnp.nf, that runs in parallel with the main mycosnp.nf code and conducts de novo assembly with Spades, followed by comparisons with Sourmash, and report generation.
Summary of changes
Added several new modules for sourmash ANI subworkflow, part of species/clade assignment for C. auris
Includes new modules for Spades de novo genome assembly, which runs in parallel to the main mycosnp.nf workflow.
Added a small number of sourmash signature files (these are mash sketches) for sourmash workflow to assets
Incorporated code to run de novo assembly and sourmash workflow into pre_mycosnp.nf file.
New feature adds a simple csv report (+MultiQC elements) to the outputs from pre_mycosnp.nf workflow
Merging Charlotte's (@royercj)
pre-mycosnpworkflow code additions working towards automated reference genome selection and clade assignment. These elements build out new feature functionality based on average nucleotide identity (ANI) computed by the program Sourmash to determine a species classification for new genomes, as well as a clade assignment for C. auris. These new features are part of a workflowpre_mycosnp.nf, that runs in parallel with the mainmycosnp.nfcode and conducts de novo assembly with Spades, followed by comparisons with Sourmash, and report generation.Summary of changes
mycosnp.nfworkflow.assetspre_mycosnp.nffile.csvreport (+MultiQC elements) to the outputs frompre_mycosnp.nfworkflow