Nextflow Registry | nf-core/popscle/freemuxlet@0.0.0-e2d3f0d

nf-core/popscle/freemuxlet @ 0.0.0-e2d3f0d

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-e2d3f0d

Total downloads: 2

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-e2d3f0d
Commit ID	e2d3f0ddf4a74a4a9031f3caea2e9deaec5a440b
Release Date	28 Apr 2026 21:15:52 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fpopscle%2Ffreemuxlet/0.0.0-e2d3f0d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/popscle/freemuxlet/blobs/sha256:3a1dbec306bb6aa39ca6205069a2b7e8797c711cf8b53484e2ebd6aa31303063
Size	3.1 KB
Checksum	sha256:3a1dbec306bb6aa39ca6205069a2b7e8797c711cf8b53484e2ebd6aa31303063
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-e2d3f0d	28 Apr 2026 21:15:52 (UTC)		1	3.1 KB	↔
0.0.0-0c7146d	08 Apr 2026 19:04:55 (UTC)