Nextflow Registry | nf-core/sequencetools/pileupcaller@0.0.0-3fc6d40

nf-core/sequencetools/pileupcaller @ 0.0.0-3fc6d40

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

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

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	0.0.0-3fc6d40
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	22 Apr 2026 15:30:49 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsequencetools%2Fpileupcaller/0.0.0-3fc6d40/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sequencetools/pileupcaller/blobs/sha256:4bf1ad509ee023e7135e6ed49cbea396b8d7ebeb5a34b119aa77dc6c4162d5dd
Size	3.3 KB
Checksum	sha256:4bf1ad509ee023e7135e6ed49cbea396b8d7ebeb5a34b119aa77dc6c4162d5dd
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:44:55 (UTC)		3	3.3 KB
0.0.0-3fc6d40	22 Apr 2026 15:30:49 (UTC)