Nextflow Registry | nf-core/popscle/dscpileup@0.0.0-0c7146d

nf-core/popscle/dscpileup @ 0.0.0-0c7146d

Software to pileup reads and corresponding base quality for each overlapping SNPs and each barcode.

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @mari-ga @maxozo @wxicu @Zethson

Maintainers: @mari-ga @maxozo @wxicu @Zethson

Software to pileup reads and corresponding base quality for each overlapping SNPs and each barcode.

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

include { POPSCLE_DSCPILEUP } from 'nf-core/popscle/dscpileup'

MIT License

Process

`Name`	`POPSCLE_DSCPILEUP`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`bam` file	Input SAM/BAM/CRAM file produced by the standard 10x sequencing platform, or any other barcoded single cell RNA-seq. `*.{bam,cram,sam}`
`vcf` file	Input VCF/BCF file files containing (AC) and (AN) from referenced population (e.g. 1000g). `*.{vcf,bcf}`

Output 5 channels

#1 cel tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`*.cel.gz` file	Contains the relation between numerated barcode ID and barcode and the number of SNP and number of UMI for each barcoded droplet. `*.cel.gz`

#2 plp tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`*.plp.gz` file	Contains the overlapping SNP and the corresponding read and base quality for each barcode ID. `*.plp.gz`

#3 umi tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`*.umi.gz` file	Contains the position covered by each umi. `*.umi.gz`

#4 var tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`*.var.gz` file	Contains the position, reference allele and allele frequency for each SNP. `*.var.gz`

#5 versions

`versions.yml` file	File containing software versions `versions.yml`

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	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:28:06 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fpopscle%2Fdscpileup/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/popscle/dscpileup/blobs/sha256:08427f1ff49f66b9ee8ebe975dd5a095c92f35d33e9c9786e4e7da0c8e391926
Size	2.7 KB
Checksum	sha256:08427f1ff49f66b9ee8ebe975dd5a095c92f35d33e9c9786e4e7da0c8e391926
Downloads	2

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:38:13 (UTC)	3	2.7 KB
0.0.0-3fc6d40	22 Apr 2026 15:27:22 (UTC)	3	2.7 KB
0.0.0-0c7146d	08 Apr 2026 19:28:06 (UTC)	2	2.7 KB