MycoSNP-WDL Workflow Series

Quick Facts

Workflow Type	Applicable Kingdom	Last Known Changes	Command-line Compatibility	Workflow Level
mycosnp_variants	Fungi	v1.5	Yes	Sample-level
mycosnp_tree	Fungi	v1.5	Yes	Set-level

MycoSNP-WDL

WDL wrappers of CDCGov/mycosnp-nf designed for Terra.bio integration. These workflows conduct Candiozyma (Candida) auris variant calling and subsequent single nucleotide polymorphism (SNP) phylogenetic tree reconstruction.

wf_mycosnp_variants.wdl

mycosnp_variants calls variants for inputted reads referencing the C. auris B11204 assembly accession GCA_016772135 by default. Users can optionally reference a separate C. auris clade data directory, FASTA, or directory as described below.

Note that mycosnp_tree requires at least 4 genomes that reference the same reference in mycosnp_variants.

Inputs

• reference optionally takes a presupplied reference clade directory depicted here. The default is GCA_016772135.
• ref_fasta optionally takes a reference FASTA (requires suffix .fa) that will be indexed via BWA and generate a reference directory.
• ref_tar optionally takes a gzipped tarchive (.tar.gz) with the same directory structure as the provided reference clades:

data/reference
├── B11221                      # Prebuilt clade directory
├── Clade1
│   ├── bwa
|   |   ├── bwa                 # BWA index for alignment 
|   |   |   ├── reference.am
|   |   |   ├── reference.ann
|   |   |   ├── reference.bwt
|   |   |   ├── reference.pac
|   |   |   └── reference.sa
│   ├── dict                    
|   |   └── reference.dict      # Picard dictionary
│   ├── fai                     
|   |   └── reference.fa.fai    # FASTA index file
│   ├── masked                  
|   |   └── reference.fa        # Masked reference sequence
│   └── Clade1.fasta
├── Clade2
├── Clade3
├── Clade4
├── Clade5
└── GCA_016772135               # Default reference

• strain optionally delineates the strain name for VCF gene name annotation. MycoSNP currently only annotates with respect to the default strain, "B11205", so changing this option will simply bypass VCF annotation.

Terra Task Name	Variable	Type	Description	Default Value	Terra Status
mycosnp_variants	read1	File	Illumina forward read file in FASTQ format (compression optional)		Required
mycosnp_variants	read2	File	Illumina reverse read file in FASTQ format (compression optional)		Required
mycosnp_variants	samplename	String	Name of sample to be analyzed		Required
mycosnp	coverage	Int	Coverage is used to calculate a down-sampling rate that results in the specified coverage. For example, if coverage is 70, then FASTQ files are down-sampled such that, when aligned to the reference, the result is approximately 70x coverage	0	Optional
mycosnp	cpu	Int	Number of CPUs to allocate to the task	8	Optional
mycosnp	debug	Boolean	If true, keeps .nextflow/ and work/ directories	false	Optional
mycosnp	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional
mycosnp	docker	String	The Docker container to use for the task	"us-docker.pkg.dev/general-theiagen/theiagen/mycosnp:1.5"	Optional
mycosnp	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	64	Optional
mycosnp	min_depth	Int	Min depth for a base to be called as the consensus sequence, otherwise it will be called as an N; set to 0 to disable	10	Optional
mycosnp	reference	String	Reference clade	"GCA_016772135"	Optional
mycosnp	sample_ploidy	Int	1	Ploidy of sample (GATK)	Optional
mycosnp	strain	String	Reference strain	"B11205"	Optional
mycosnp_variants	ref_fasta	File	Reference FASTA file		Optional
mycosnp_variants	ref_tar	File	Reference gzipped compressed tarchive		Optional
version_capture	timezone	String	Alternative timezone		Optional

Outputs

Variable	Type	Description
analysis_date	String	Date of the analysis
assembly_size	Int	Size of the assembly
average_q_score_after_trimming	Float	Average quality score after trimming
average_q_score_before_trimming	Float	Average quality score before trimming
consensus_n_variant_min_depth	Int	Minimum depth for consensus N variant
full_results	File	Full results file
gc_after_trimming	Float	GC content after trimming
gc_before_trimming	Float	GC content before trimming
mean_coverage_depth	Float	Mean coverage depth
multiqc	File	MultiQC report
myco_bam	File	BAM file
myco_bam_bai	File	BAM index file
mycosnp_docker	String	Docker image used for MycoSNP
mycosnp_variants_analysis_date	String	Date of the MycoSNP variants analysis
mycosnp_variants_version	String	Version of the MycoSNP variants
mycosnp_version	String	Version of MycoSNP
number_n	Int	Number of N bases
paired_reads_after_trimming	Int	Number of paired reads after trimming
paired_reads_after_trimming_percent	String	Percentage of paired reads after trimming
percent_reference_coverage	Float	Percentage of reference coverage
reads_after_trimming	Int	Number of reads after trimming
reads_after_trimming_percent	String	Percentage of reads after trimming
reads_before_trimming	Int	Number of reads before trimming
reads_mapped	Int	Number of reads mapped
reference_length_coverage_after_trimming	Float	Reference length coverage after trimming
reference_length_coverage_before_trimming	Float	Reference length coverage before trimming
reference_name	String	Name of the reference genome used
reference_strain	String	Reference strain used
unpaired_reads_after_trimming	Int	Number of unpaired reads after trimming
unpaired_reads_after_trimming_percent	String	Percentage of unpaired reads after trimming
vcf	File	Compressed variant call format (VCF) file depicting SNPs
vcf_index	File	Compressed index file for the VCF

wf_mycosnp_tree.wdl

mycosnp_tree reconstructs an IQ-TREE SNP phylogenetic tree that incorporates representative genomes of Clade1-Clade5 C. auris. VCF data generated from wf_mycosnp_variants.wdl are used as inputs.

NOTE: At least four samples, including reference, are required

Inputs

• reference optionally takes a presupplied reference clade directory delineated here.
• ref_fasta optionally takes a reference FASTA (requires suffix .fa) that will be indexed via BWA and generate a reference directory.
• strain is passed to output but does not change workflow function.

Terra Task Name	Variable	Type	Description	Default Value	Terra Status
mycosnp_tree	vcf	Array[File]	VCF files (.vcf.gz) containing SNP data for phylogenetic analysis. These files can be generated from wf_mycosnp_variants.wdl		Required
mycosnp_tree	vcf_index	Array[File]	Index files for the VCF files		Required
mycosnp_tree	ref_fasta	File	Reference FASTA input		Optional
mycosnptree	cpu	Int	Number of CPUs to allocate to the task	8	Optional
mycosnptree	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional
mycosnptree	docker	String	The Docker container to use for the task	"us-docker.pkg.dev/general-theiagen/theiagen/mycosnp:1.5"	Optional
mycosnptree	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	64	Optional
mycosnptree	reference	String	Preexisting reference directory	"GCA_016772135"	Optional
mycosnptree	strain	String	mycosnp-nf reference strain name	"B11205"	Optional
version_capture	timezone	String	Alternative timezone		Optional

Outputs

Variable	Type	Description
mycosnp_alignment	File	Concatenated SNP alignment file
mycosnp_docker	String	Docker image used for MycoSNP
mycosnp_fastree_tree	File	Phylogenetic tree inferred using FastTree (heuristic maximum likelihood)
mycosnp_iqtree_tree	File	Phylogenetic tree inferred using IQ-TREE (high quality maximum likelihood)
mycosnp_rapidnj_tree	File	Phylogenetic tree inferred using RapidNJ (neighbor-joining method)
mycosnp_tree_analysis_date	String	Date of the analysis
mycosnp_tree_full_results	File	Full results file
mycosnp_tree_vcf_csv	File	SNP variants formatted as a CSV table
mycosnp_tree_version	String	Version of the mycosnp_tree WDL workflow
mycosnp_version	String	Version of MycoSNP
mycosnptree_snpdists	File	SNP distances file
reference_name	String	Name of the reference
reference_strain	String	Reference strain used