nf-core/atlas/call @ 0.0.0-3fc6d40
Summary
generate VCF file from a BAM file using various calling methods
Get started
Add the following snippet to your workflow script to include this module.
include { ATLAS_CALL } from 'nf-core/atlas/call'
License
MIT License
Name
|
ATLAS_CALL |
|---|
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
|
|---|
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
|
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 | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:02:11 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fatlas%2Fcall/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/atlas/call/blobs/sha256:78b02921244649ea8385abed7c478a1fccb7eeb91e7bc4e91fe3b7dc9866a8a6 |
| Size | 2.8 KB |
| Checksum | sha256:78b02921244649ea8385abed7c478a1fccb7eeb91e7bc4e91fe3b7dc9866a8a6 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:02:57 (UTC) | 4 | 2.8 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:02:11 (UTC) | 3 | 2.8 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:43:35 (UTC) | 3 | 2.8 KB |