Nextflow Registry | nf-core/sequencetools/pileupcaller@0.0.0-0c7146d

nf-core/sequencetools/pileupcaller @ 0.0.0-0c7146d

PileupCaller is a tool to create genotype calls from bam files using read-sampling methods

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @TCLamnidis

Maintainers: @TCLamnidis

PileupCaller is a tool to create genotype calls from bam files using read-sampling methods

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

include { SEQUENCETOOLS_PILEUPCALLER } from 'nf-core/sequencetools/pileupcaller'

MIT License

Process

`Name`	`SEQUENCETOOLS_PILEUPCALLER`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`mpileup` file	samtools mpileup output.

`snpfile` file	Eigenstrat format .snp file of the sites in the mpileup file to call genotypes on. Only alleles matching the Ref and Alt alleles of the provided snp file will be called.

`sample_names_fn` file	File containing the sample names

Output 4 channels

#1 plink tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bed` file	A tuple containing the output Plink-formatted bed, bim and fam files. `*.{bed,bim,fam}`
`*.bim` file	A tuple containing the output Plink-formatted bed, bim and fam files. `*.{bed,bim,fam}`
`*.fam` file	A tuple containing the output Plink-formatted bed, bim and fam files. `*.{bed,bim,fam}`

#2 freqsum tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.freqsum.gz` file	The output freqsum-formatted file. `*.freqsum.gz`

#3 versions

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

#4 eigenstrat tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.geno` file	A tuple containing the output Eigenstrat-formatted geno, snp and ind files. `*.{geno,snp,ind}.txt`
`*.snp` file	A tuple containing the output Eigenstrat-formatted geno, snp and ind files. `*.{geno,snp,ind}.txt`
`*.ind` file	A tuple containing the output Eigenstrat-formatted geno, snp and ind files. `*.{geno,snp,ind}.txt`

Tool	Description	Homepage
sequencetools	Tools for population genetics on sequencing data	https://github.com/stschiff/sequenceTools

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:13:24 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fsequencetools%2Fpileupcaller/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/sequencetools/pileupcaller/blobs/sha256:cfe0c79722878fba75475c1f1aca1afc15974130263d235753534823d35cbcf3
Size	3.3 KB
Checksum	sha256:cfe0c79722878fba75475c1f1aca1afc15974130263d235753534823d35cbcf3
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:13:24 (UTC)		1	3.3 KB	-