Nextflow Registry | nf-core/atlas/call@0.0.0-0c7146d

nf-core/atlas/call @ 0.0.0-0c7146d

generate VCF file from a BAM file using various calling methods

atlas variant calling vcf population genetics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @jfy133

Maintainers: @jfy133

generate VCF file from a BAM file using various calling methods

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

include { ATLAS_CALL } from 'nf-core/atlas/call'

MIT License

Process

`Name`	`ATLAS_CALL`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	A BAM/ file `*.bam`
`bai` file	The BAI file for the input BAM file `*.bai`
`pmd` file	Optional PMD file from atlas pmd function in text format `*.txt`
`recal` file	Optional recalibration file from atlas recal function in text format `*.txt`

`fasta` file	The reference FASTA file used to generate the BAM file `*.{fasta,fna,fa}`

`fai` file	The index of the FASTA file used for to generate the BAM file `*.fai`

`known_alleles` file	Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation. `*.{txt.tsv}`

`method` string	Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation. `MLE\|Bayesian\|allelePresence\|randomBase\|majorityBase`

Output 2 channels

#1 vcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	VCF file with variant calls `*.vcf.gz`

#2 versions_atlas tuple

`${task.process}` string	The name of the process
`atlas` string	The name of the tool
`(atlas 2>&1) \| grep Atlas \| head -n 1 \| sed -e 's/^[[:space:]]*Atlas //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
atlas	ATLAS, a suite of methods to accurately genotype and estimate genetic diversity	https://bitbucket.org/wegmannlab/atlas/wiki/Home

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:23:04 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fatlas%2Fcall/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/atlas/call/blobs/sha256:1672ec7391a7c7bdebac7a3d94305067dbf82b4475cd339a568dd4c02a0395fb
Size	2.8 KB
Checksum	sha256:1672ec7391a7c7bdebac7a3d94305067dbf82b4475cd339a568dd4c02a0395fb
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:23:04 (UTC)		1	2.8 KB	-