Workflow: SVision-Pro workflow for structural variant detection in cancer samples
Fetched 2025-10-23 18:41:31 GMT
Verified with cwltool version 3.1.20230201224320
A workflow that uses SVision-Pro to identify structural variants in tumor/normal paired samples from Oxford Nanopore Technology (ONT) long-read sequencing data.
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| threads | Integer (Optional) |
Number of threads to use for alignment and SV calling |
|
| min_sv_size | Integer (Optional) |
Minimum structural variant size to detect |
|
| tumor_reads | File [null] |
Tumor sample ONT reads in FASTQ or BAM format |
|
| normal_reads | File [null] |
Normal/control sample ONT reads in FASTQ or BAM format |
|
| output_prefix | String |
Prefix for output files |
|
| reference_genome | File [null] |
Reference genome in FASTA format |
|
| min_support_reads | Integer (Optional) |
Minimum number of supporting reads required for SV calling |
|
| reference_genome_index | File (Optional) |
Index file for reference genome (.fai) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| align_tumor |
minimap2-align.cwl
(CommandLineTool)
|
Minimap2 long read alignment tool |
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. It is particularly optimized for Oxford Nanopore and PacBio reads. |
| align_normal |
minimap2-align.cwl
(CommandLineTool)
|
Minimap2 long read alignment tool |
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. It is particularly optimized for Oxford Nanopore and PacBio reads. |
| index_reference |
samtools-faidx.cwl
(CommandLineTool)
|
Samtools faidx index generator |
Tool to generate FASTA index files using samtools faidx |
| run_svisionpro_somatic |
svisionpro-somatic.cwl
(CommandLineTool)
|
SVision-Pro somatic structural variant caller |
SVision-Pro is a structural variant (SV) caller designed for long-read sequencing data, with special optimization for Oxford Nanopore Technology reads. This tool definition is for somatic variant calling using tumor-normal paired samples. |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| sv_vcf | File | ||
| sv_report | File | ||
| tumor_bam | File | ||
| normal_bam | File |
https://w3id.org/cwl/view/git/d2bc378c641529cd8ff176673fe17f9ce152ca2f/workflow/main.cwl
