MycoSNP-WDL Workflow Series

Quick Facts

Workflow Type	Applicable Kingdom	MycoSNP-WDL version	MycoSNP-NF Version	Command-line Compatibility	Workflow Level
mycosnp_variants	Fungi	v1.6.2-wdl	v1.6.3	Yes	Sample-level
mycosnp_tree	Fungi	v1.6.2-wdl	v1.6.3	Yes	Set-level

MycoSNP-WDL

MycoSNP-WDL is a repository comprised of WDL wrappers of CDCGov/mycosnp-nf to enable MycoSNP use on Terra.bio. These workflows conduct Candiozyma (Candida) auris variant calling and subsequent single nucleotide polymorphism (SNP) phylogenetic tree reconstruction.

MycoSNP-WDL v. MycoSNP-NF

MycoSNP-NF is the source Nextflow code for analysis. MycoSNP-WDL's version naming scheme intends to remain concordant with the MycoSNP-NF version contained ONLY to the minor release version. Patch release versions may be discrepant. For example, MycoSNP-WDL v1.6.2 contains source code MycoSNP-NF v1.6.3. Please see the table above for version coordination.

wf_mycosnp_variants.wdl

mycosnp_variants calls variants for inputted reads referencing the C. auris Clade I B11205 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

Inputting a reference genome is required to run mycosnp_variants. By default, the reference will be set to "Clade1". The reference can be set by one of the following inputs:

• reference optionally takes a presupplied reference clade directory depicted here. These references are derived from GenBank assemblies:

Reference Input	Assembly Accession
Clade1	GCA_016772135.1
Clade2	GCA_003013715.1
Clade3	GCA_002775015.1
Clade4	GCA_003014415.1
Clade5	GCA_016809505.1
Clade6	GCA_032714025.1

• ref_fasta optionally takes a reference FASTA (requires suffix .fa) that will be indexed via BWA to 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
├── 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
├── Clade6

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-wdl:1.6.2"	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	"Clade1"	Optional
mycosnp	ref_fasta	File	Reference FASTA file		Optional
mycosnp	ref_tar	File	Reference gzipped compressed tarchive		Optional
mycosnp	sample_ploidy	Int	1	Ploidy of sample (GATK)	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 clade/input 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-Clade6 C. auris. VCF data generated from wf_mycosnp_variants.wdl are used as inputs.

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

Inputs

Inputting a reference genome is required to run mycosnp_tree. By default, the reference will be set to "Clade1". The reference can be set by one of the following 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.

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
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-wdl:1.6.2"	Optional
mycosnptree	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	64	Optional
mycosnptree	reference	String	Preexisting reference directory	"Clade1"	Optional
mycosnptree	ref_fasta	File	Reference FASTA input		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 clade/input used