Nextflow Registry | nf-core/poolsnp@0.0.0-6c4ed3a

nf-core/poolsnp @ 0.0.0-6c4ed3a

PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs.

poolseq mpileup variant-calling

Latest version: 0.0.0-6c4ed3a

Total downloads: 11

Source: nf-core/modules

Authors: @abhilesh

Maintainers: @abhilesh

PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs.

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

include { POOLSNP } from 'nf-core/poolsnp'

MIT License

Process

`Name`	`POOLSNP`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information. e.g. `[ id:'sample1', single_end:false ]`
`mpileup` file	MPILEUP file. This file contains the base calls and alignment information for each position in the reference genome. It is used as input for variant calling and other downstream analyses. `*.mpileup`

#2 tuple

`meta2` map	Groovy Map containing sample information. e.g. `[ id:'sample1' ]`
`reference` file	Reference genome in FASTA format. May NOT contain any special characters such as "/\|,:" `*.{fasta,fa}`

#3 tuple

`meta3` map	Groovy Map containing sample information. e.g. `[ id:'sample1', single_end:false ]`
`max_cov` float	Maximum coverage is calculated for every library and chromosomal arm as the percentile of a coverage distribution, e.g. max-cov=0.98 will only consider positions within the 98% coverage percentile for a given sample and chromosomal arm. Note: Provide `max_cov` or `max_cov_file` but not both. Read more: https://github.com/capoony/PoolSNP
`max_cov_file` file	File containing the maximum coverage thresholds for all chromosomal arms and libraries. This file needs to be tab-delimited with two columns: Chromosomal name Comma-separated list of coverage thresholds for each sample in the mpileup file. e.g. `2L 100,100,100,200,200` would mean a threshold of 100 for the first three samples and 200 for the last two samples on chromosomal arm 2L. Note: Provide `max_cov` or `max_cov_file` but not both. Read more: https://github.com/capoony/PoolSNP

Output 4 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.vcf.gz` file	Gzipped VCF file containing allele counts and frequencies for every position and library `*.vcf.gz`

#2 max_cov tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`cov-.txt` file	File containing the maximum coverage thresholds for all chromosomal arms and libraries `cov-.txt`

#3 versions

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

#4 bad_sites tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*BS.txt.gz` file	File containing a list of sites (variable and invariable) that did not pass the SNP calling criteria `*BS.txt.gz`

Tool	Description	Homepage
poolsnp	PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs.	https://github.com/capoony/PoolSNP

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:38:10 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fpoolsnp/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/poolsnp/blobs/sha256:6e8d30ca908488d5dc9952f38744784c5b84c773f8aebb35270e571dbd53a323
Size	3.6 KB
Checksum	sha256:6e8d30ca908488d5dc9952f38744784c5b84c773f8aebb35270e571dbd53a323
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:38:10 (UTC)		4	3.6 KB
0.0.0-3fc6d40	22 Apr 2026 15:27:19 (UTC)		4