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nf-core/canvas/germline @ 0.0.0-6c4ed3a

Calls germline copy number variants (CNVs) from whole genome sequencing data using Illumina Canvas in SmallPedigree-WGS mode. Although named SmallPedigree-WGS, this mode is recommended for single germline samples as well as small pedigrees. The module accepts aligned reads (BAM), germline SNV calls, and sex-specific ploidy information, and outputs a VCF with copy number status across the genome together with a coverage-and-variant-frequency file used for downstream segmentation.

CNV copy number variants germline WGS canvas
Latest version: 0.0.0-6c4ed3a
Total downloads: 3
Source: nf-core/modules
Authors: @ktruve
Maintainers: @ktruve

Summary

Calls germline copy number variants (CNVs) from whole genome sequencing data using Illumina Canvas in SmallPedigree-WGS mode. Although named SmallPedigree-WGS, this mode is recommended for single germline samples as well as small pedigrees. The module accepts aligned reads (BAM), germline SNV calls, and sex-specific ploidy information, and outputs a VCF with copy number status across the genome together with a coverage-and-variant-frequency file used for downstream segmentation.

Get started

Add the following snippet to your workflow script to include this module.

include { CANVAS_GERMLINE } from 'nf-core/canvas/germline'

License

MIT License

Process
Name CANVAS_GERMLINE
Input 6 channels
#1 tuple
meta map

Groovy Map containing sample information. e.g. [ id:'sample1' ]
bam file

Sorted BAM file of aligned WGS reads.

 *.bam
bai file

BAM index file.

 *.bai
germline_snv_vcf file

VCF (or gzipped VCF) containing germline SNV b-allele sites (PASS filter only). Typically produced by a variant caller such as DNAscope or DeepVariant.

 *.{vcf,vcf.gz}
#3 tuple
sex string

Sample sex. Must be either "male" or "female". Used to select the appropriate ploidy VCF for sex chromosomes.
male_ploidy_vcf file

VCF defining expected ploidy for sex chromosomes in male samples. Both ploidy VCFs (male and female) must always be provided. The module automatically selects the correct one based on the sex value. The sample name in the VCF header is automatically updated to match the SM tag in the BAM header. Expected format (hg38 example):

##fileformat=VCFv4.1
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
#CHROM  POS      ID  REF  ALT    QUAL  FILTER  INFO              FORMAT  SAMPLE
chrX    0        .   N    <CNV>  .     PASS    END=10001         CN      1
chrX    2781479  .   N    <CNV>  .     PASS    END=155701383     CN      1
chrX    156030895 .  N    <CNV>  .     PASS    END=156040895     CN      1
chrY    0        .   N    <CNV>  .     PASS    END=57227415      CN      1
*.vcf
female_ploidy_vcf file

VCF defining expected ploidy for sex chromosomes in female samples. Both ploidy VCFs (male and female) must always be provided. The module automatically selects the correct one based on the sex value. The sample name in the VCF header is automatically updated to match the SM tag in the BAM header. Expected format (hg38 example):

##fileformat=VCFv4.1
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
#CHROM  POS  ID  REF  ALT    QUAL  FILTER  INFO          FORMAT  SAMPLE
chrY    0    .   N    <CNV>  .     PASS    END=57227415  CN      0
*.vcf
genomedir directory

Canvas genome reference directory containing genome.fa and GenomeSize.xml. Available for GRCh37/hg19/GRCh38 from s3://canvas-cnv-public.
reference file

Canvas-ready kmer reference file (kmer.fa). Available from s3://canvas-cnv-public.

 *.fa
filter13 file

BED file of regions to exclude from CNV calling (e.g. centromeres, telomeres). Named filter13 following Canvas reference package conventions. Available from s3://canvas-cnv-public.

 *.bed
Output 3 channels
#1 vcf tuple
meta map

Groovy Map containing sample information. e.g. [ id:'sample1' ]
${prefix}.vcf.gz file

Bgzipped VCF file containing germline CNV calls. Canvas:REF entries (non-variant regions) are excluded. Requires further annotation for standard SV ALT notation.

 *.vcf.gz
#2 covandvarfreq tuple
meta map

Groovy Map containing sample information. e.g. [ id:'sample1' ]
${prefix}.CoverageAndVariantFrequency.txt file

Tab-separated file with per-bin coverage and variant allele frequency values. Used as input for CANVAS_CREATESEG to generate segmentation files.

 *.CoverageAndVariantFrequency.txt
#3 versions_canvas tuple
${task.process} string

The name of the process
canvas string

The name of the tool
1.40.0 string

The version of the tool (hardcoded as Canvas is an archived tool)
Tool Description Homepage
canvas Canvas is a tool for calling copy number variants (CNVs) from human DNA sequencing data. https://github.com/Illumina/canvas
Version 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:08:28 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fcanvas%2Fgermline/0.0.0-6c4ed3a/download