A rocker/r-ver:4.4.0 container with vcfR R-package (and some dependencies). Mainly used for variant calling mutagenesis analysis.

Note

Every push to main automatically builds and pushes the image to GitHub Container Registry. Tagged releases (e.g. v1.0.0) produce versioned image tags.

Included softwares

• vcfR
• tidyverse
• data.table
• clinfun
• R.utils
• git
• less

Pull the container

# As docker
docker pull ghcr.io/karlssonlaboratory/variant_call:530cf28

# As apptainer
apptainer pull docker://ghcr.io/karlssonlaboratory/variant_call:530cf28

# As singularity
singularity pull docker://ghcr.io/karlssonlaboratory/variant_call:530cf28

Run interactively

docker run -it --rm -v $(pwd):/data ghcr.io/karlssonlaboratory/variant_call:530cf28

Build locally

git clone https://github.com/karlssonlaboratory/variant_call:530cf28.git
cd variant_call
docker build -t variant_call .

As nextflow process

process PROCESS_NAME {
	
	. . .

	container "${workflow.containerEngine == 'singularity' ?
  	'docker://ghcr.io/karlssonlaboratory/variant_call:530cf28' :
  	'ghcr.io/karlssonlaboratory/variant_call:530cf28'}"

  . . .
}

The container definition uses an elvis operator = <statement> ? <TRUE> : <FALSE>