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

Included softwares

• vcfR
• tidyverse
• patchwork
• data.table
• clinfun
• R.utils
• git
• less
• procps (useful inside Nextflow pipelines)

Pull the container

# As docker
docker pull ghcr.io/karlssonlaboratory/variant_calling:f23646d

# As apptainer
apptainer pull docker://ghcr.io/karlssonlaboratory/variant_calling:f23646d

# As singularity
singularity pull docker://ghcr.io/karlssonlaboratory/variant_calling:f23646d

Run interactively

docker run -it --rm -v $(pwd):/data ghcr.io/karlssonlaboratory/variant_calling:f23646d

Build locally

git clone https://github.com/karlssonlaboratory/variant_calling:f23646d.git
cd variant_calling
docker build -t variant_calling .

As nextflow process

process PROCESS_NAME {
	
	. . .

	container "${workflow.containerEngine == 'singularity' ?
    'docker://ghcr.io/karlssonlaboratory/variant_calling:f23646d' :
    'ghcr.io/karlssonlaboratory/variant_calling:f23646d'}"

  . . .
}

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

Dockerfile details

Dockerfile runs the content inside install.R, which holds all R-packages. Edit this file in order to add more packages

# Dockerfile
COPY install.R /tmp/install.R
RUN Rscript /tmp/install.R

# install.R
pkgs_CRAN <- c(
  "data.table",
  "tidyverse"
  "patchwork",
  "vcfR",
  "clinfun",
  "R.utils"
)

install.packages(
  pkgs_CRAN,
  repos = getOption("repos"),
  Ncpus = parallel::detectCores()
)