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nf-core/popscle/freemuxlet @ 0.0.0-3fc6d40

Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is not available.

popscle demultiplexing genotype-based deconvoltion single cell
Latest version: 0.0.0-6c4ed3a
Total downloads: 10
Source: nf-core/modules
Authors: @wxicu
Maintainers: @wxicu

Summary

Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is not available.

Get started

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

include { POPSCLE_FREEMUXLET } from 'nf-core/popscle/freemuxlet'

License

MIT License

Process
Name POPSCLE_FREEMUXLET
Input 1 channel
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1']
plp directory

Directory contains pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup.
n_sample integer

Number of samples multiplexed together.
Output 6 channels
#1 vcf tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.clust1.vcf.gz file

Output vcf file for each sample inferred and clustered from freemuxlet.

 *.clust1.vcf.gz
#2 lmix tuple
meta map

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

Output file contains basic statistics for each barcode.

 *.lmix
#3 result tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.clust1.samples.gz file

Output file contains the best guess of the sample identity, with detailed statistics to reach to the best guess.

 *.clust1.samples.gz
#4 versions
versions.yml file

File containing software versions

 versions.yml
#5 singlet_vcf tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.clust0.vcf.gz file

Optional output vcf file for each sample inferred and clustered from freemuxlet assuming all droplets are singlets when writing auxiliary output files is turned on.

 *.clust0.vcf.gz
#6 singlet_result tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
*.clust0.samples.gz file

Optional output file contains the best sample identity assuming all droplets are singlets when writing auxiliary output files is turned on.

 *.clust0.samples.gz
Tool Description Homepage
popscle A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxiliary tools https://github.com/statgen/popscle
Version 0.0.0-3fc6d40
Commit ID 6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date 22 Apr 2026 15:27:23 (UTC)
Download URL https://registry.nextflow.io/api/v1/modules/nf-core%2Fpopscle%2Ffreemuxlet/0.0.0-3fc6d40/download
OCI Store URL https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/popscle/freemuxlet/blobs/sha256:79ab786ac39efbf0aaceed199be85c679c27045107a8ecd4f5b041e9af213fdb
Size 3.1 KB
Checksum sha256:79ab786ac39efbf0aaceed199be85c679c27045107a8ecd4f5b041e9af213fdb
Downloads 3
Version Date Status Downloads Size
0.0.0-6c4ed3a 23 Apr 2026 15:38:14 (UTC) 3 3.1 KB
0.0.0-3fc6d40 22 Apr 2026 15:27:23 (UTC) 3 3.1 KB
0.0.0-0c7146d