nf-core/angsd/contamination @ 0.0.0-0c7146d
Summary
A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome.
Get started
Add the following snippet to your workflow script to include this module.
include { ANGSD_CONTAMINATION } from 'nf-core/angsd/contamination'
License
MIT License
Process
Name
|
ANGSD_CONTAMINATION |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
icounts
file
|
Internal format for dumping binary single chrs. Useful for ANGSD contamination *.icnts.gz
|
#2
tuple
meta2
map
|
Groovy Map containing information related to the hapmap_file. e.g. [ id:'test' ] |
|---|---|
hapmap_file
file
|
A list of variable sites to look for heterozygosity. |
Output
2 channels
#1
txt
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.txt
file
|
Contamination estimation output. *.txt
|
#2
versions_angsd
tuple
${task.process}
string
|
The name of the process |
|---|---|
angsd
string
|
The name of the tool |
angsd 2>&1 | sed '1!d;s/.*version: //;s/ .*//'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| angsd | ANGSD: Analysis of next generation Sequencing Data | http://www.popgen.dk/angsd/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:22:12 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fangsd%2Fcontamination/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/angsd/contamination/blobs/sha256:88fb467c52bf80c1f864f1c273488a0e9305ae85af2cfb09a21f88c9e34828c1 |
| Size | 2.6 KB |
| Checksum | sha256:88fb467c52bf80c1f864f1c273488a0e9305ae85af2cfb09a21f88c9e34828c1 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:22:12 (UTC) | 1 | 2.6 KB | - |