RefNAAP-wdl

WDL wrapper around RefNAAP for execution on Terra.bio.

What is RefNAAP?

RefNAAP is a reference based Oxford Nanopore Technologies (ONT) assembly analysis pipeline for RABV genomes. In summary, it performs the following steps:

1. t QCs the files using fastQC and multiQC to generate a quality report.
2. It trims the left and right ends of the reads by 25 basepairs, and filters out reads shorter than 50bp. These values can be costumized.
3. It generates the assembly reads using reference-based assembly with minimap2, gap fixing, and medaka.

It uses a reference file composed of 14 different RABV sequences for the reference-based assembly.

How do i use RefNAAP on Terra?

RefNAAP-wdl is available on Terra.bio, a cloud-native platform for researchers to access data, run analysis tools, and collaborate. With Terra.bio, you can easily process your data without prior knowledge of the command-line.

The following steps, assume you have already set up an account on Terra.bio and created a workspace to work with RefNAAP-wdl.

Import the workflow from Dockstore

To begin using RefNAAP-wdl on Terra.bio, you will need to import the workflow from Dockstore, which is available at: RefNAAP-wdl Dockstore Import.

Figure 1: RefNAAP-wdl on Dockstore.

Once you are on the Dockstore page for RefNAAP-wdl, you will want to locate the Launch with section on the right side of the page and click on Terra.

Figure 2: Launching a workflow with Terra.bio on Dockstore.

After clicking the Terra button, you will be transported to Terra.bio. Once here you will decide on the Destination Workspace. Please select which of your workspaces you would like to import this workflow into. Once you have selected a Destination Workspace, all that remains is to click the Import button.

Figure 3: Importing workflow interface on Terra.bio.

Workflow configuration on Terra.bio

The RefNAAP-wdl should now be available in Terra.bio on the WORKFLOWS tab. When clicking on the RefNAAP-wdl the workflow interface loads. On the workflow configuration section you will need to select the Run workflow(s) with inputs defined by data table. RefNAAP-wdl is a sample-level workflow.

Figure 4: RefNAAP-wdl on Terra.bio.

Workflow inputs

Several inputs are available for workflow costumization: required inputs that are necessary for execution, and optional inputs that have default values but can be overwritten by the user.

Note: To provide inputs from the data table, terra uses the this.{column_name} notation. For example, to pass the ONT reads that are in the ont_read column on the data table to the read1 input, the value should be passed as this.ont_reads.

Figure 5: RefNAAP-wdl inputs.

Table 1: Input description for RefNAAP-wdl

Terra Task Name	Variable	Type	Description	Default Value	Terra Status
refnaap_wf	read1	File	Base-called ONT read file in FASTQ file format (compressed)		Required
refnaap_wf	samplename	String	Name of sample to be analyzed		Required
refnaap	cpu	Int	Number of CPUs to allocate to the task	8	Optional
refnaap	disk_size	Int	Amount of storage (in GB) to allocate to the task	100	Optional
refnaap	docker	String	The Docker container to use for the task	"us-docker.pkg.dev/general-theiagen/internal/refnaap:b3ad097"	Optional
refnaap	memory	Int	Amount of memory/RAM (in GB) to allocate to the task	16	Optional
refnaap	min_coverage	Int	Amplicon regions need a minimum of this average coverage number	5	Optional
refnaap	model	String	Basecall model	"r10_min_high_g303"	Optional
refnaap	size	Int	Filter reads less than this length	50	Optional
refnaap	trim_left	Int	Bases to trim from left side of read	25	Optional
refnaap	trim_right	Int	Bases to trim from right side of read	25	Optional

Note: Available basecall models:

r103_min_high_g345, r103_min_high_g360, r103_prom_high_g360, r103_prom_snp_g3210, r103_prom_variant_g3210, r10_min_high_g303, r10_min_high_g340, r941_min_fast_g303, r941_min_high_g303, r941_min_high_g330, r941_min_high_g340_rle, r941_min_high_g344, r941_min_high_g351, r941_min_high_g360, r941_prom_fast_g303, r941_prom_high_g303, r941_prom_high_g330, r941_prom_high_g344, r941_prom_high_g360, r941_prom_high_g4011, r941_prom_snp_g303, r941_prom_snp_g322, r941_prom_snp_g360, r941_prom_variant_g303, r941_prom_variant_g322, r941_prom_variant_g360

Workflow outputs

The RefNAAP-wdl produces four outputs that are populated back to the data table.

Figure 5: RefNAAP-wdl outputs.

Table 2: Output description for RefNAAP-wdl

Variable	Type	Description
refnaap_analysis_date	String	Date of analysis with RefNAAP.
refnaap_assembly_fasta	File	Consensus assembly generated by RefNAAP in FASTA format.
refnaap_docker	String	Dockerfile used.
refnaap_multiqc_report	File	MultiQC report generated by RefNAAP in HTML format.

Contact

If you have any questions or concerns, please raise a GitHub issue or email Theiagen's general support at [email protected].