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nf-core/cellsnp/modea @ 0.0.0-6c4ed3a

Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use the mode A of cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs for droplet based single cell data.

genotyping single cell SNP droplet based single cells
Latest version: 0.0.0-6c4ed3a
Total downloads: 9
Source: nf-core/modules
Authors: @wxicu
Maintainers: @wxicu

Summary

Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use the mode A of cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs for droplet based single cell data.

Get started

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

include { CELLSNP_MODEA } from 'nf-core/cellsnp/modea'

License

MIT License

Process
Name CELLSNP_MODEA
Input 1 channel
#1 tuple
meta map

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

A single BAM/SAM/CRAM file, e.g., from CellRanger.

 *.{bam,cram,sam}
bai file

The index of the BAM/CRAM file.

 *.{bai,crai}
region_vcf file

A optional vcf file listing all candidate SNPs for genotyping.

 *.{vcf, vcf.gz}
barcode file

A plain file listing all effective cell barcodes.

 *.tsv
Output 7 channels
#1 base tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.base.vcf.gz file

A VCF file listing genotyped SNPs and aggregated AD & DP information (without GT).

 *.base.vcf.gz
#2 cell tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.cells.vcf.gz file

A VCF file listing genotyped SNPs and aggregated AD & DP information & genotype (GT) information for each cell or sample.

 *.cells.vcf.gz
#3 sample tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.samples.tsv file

A TSV file listing cell barcodes or sample IDs.

 *.tsv
#4 depth_other tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.tag.OTH.mtx file

A file in “Matrix Market exchange formats”, containing the sum of allele depths of all the alleles other than REF and ALT.

 *.tag.OTH.mtx
#5 allele_depth tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.tag.AD.mtx file

A file in “Matrix Market exchange formats”, containing the allele depths of the alternative (ALT) alleles.

 *.tag.AD.mtx
#6 depth_coverage tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.tag.DP.mtx file

A file in “Matrix Market exchange formats”, containing the sum of allele depths of the reference and alternative alleles (REF + ALT).

 *.tag.DP.mtx
#7 versions_cellsnp tuple
${task.process} string

The name of the process
cellsnp string

The name of the tool
cellsnp-lite --v | cut -f2 -d ' ' eval

The expression to obtain the version of the tool
Tool Description Homepage
cellsnp Efficient genotyping bi-allelic SNPs on single cells https://github.com/single-cell-genetics/cellsnp-lite
Version 0.0.0-6c4ed3a
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 23 Apr 2026 15:08:48 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fcellsnp%2Fmodea/0.0.0-6c4ed3a/download