CONTAINERS.md

Containers

Our main container is designed using Bioconda to install all tools used in Sarek:

• sarek

For annotation, the main container can be used, but the cache has to be downloaded, or additional containers are available with cache (see annotation guide):

• For GRCh37:
  • snpeffgrch37
  • vepgrch37
• For GRCh38:
  • snpeffgrch38
  • vepgrch38

What is actually inside the containers

sarek

• Based on nfcore/base:latest
• Contain AlleleCount 2.1.2
• Contain BCFTools 1.9
• Contain BWA 0.7.17
• Contain FastQC 0.11.8
• Contain FreeBayes 1.2.0
• Contain GATK4 4.1.1.0
• Contain GeneSplicer 1.0
• Contain HTSlib 1.9
• Contain IGVtools 2.3.93
• Contain Manta 1.5.0
• Contain MultiQC 1.7
• Contain Qualimap 2.2.2b
• Contain R 3.5.1
• Contain RColorBrewer 1.1
• Contain Rtracklayer 1.42.1
• Contain samtools 1.9
• Contain snpEff 4.3.1t
• Contain Strelka2 2.9.3
• Contain VCFanno 0.3.1
• Contain VCFtools 0.1.16
• Contain VEP 96.0

snpeffgrch37

• Based on nfcore/base:latest
• Contain snpEff 4.3.1t
• Contain cache for GRCh37.75

snpeffgrch38

• Based on nfcore/base:latest
• Contain snpEff 4.3.1t
• Contain cache for GRCh38.86

vepgrch37

• Based on nfcore/base:latest
• Contain GeneSplicer 1.0
• Contain VEP 96.0
• Contain cache for GRCh37 version 96

vepgrch38

• Based on nfcore/base:latest
• Contain GeneSplicer 1.0
• Contain VEP 96.0
• Contain cache for GRCh38 version 96

Building

A Nextflow script is provided to build and/or push containers from Docker, or build for Singularity.

Usage

nextflow run build.nf [--docker] [--singularity] /
[--containerPath <path>] [--push] [--containers <container1[,container2..]>] /
[--repository <repository>] [--tag tag]

• --containers: Choose which containers to build. Default: all. Possible values (to separate by commas):

  • all - all available containers.
  • sarek - the sarek container.
  • snpeffgrch37 - the snpeffgrch37 container.
  • snpeffgrch38 - the snpeffgrch38 container.
  • vepgrch37 - the vepgrch37 container.
  • vepgrch38 - the vepgrch38 container.

• --docker: Build containers using Docker

• --push: Push containers to DockerHub

• --repository: Build containers under given repository. Default: maxulysse

• --singularity: Build containers using Singularity.

• --containerPath: Select where to download containers. Default: $PWD

• --tag: Build containers using given tag. Default is version number.

Example

nextflow run build.nf --docker --singularity --push --containers sarek

For lazy users

We provide script to build/push or pull all containers

./scripts/do_all.sh        # Build all docker containers
./scripts/do_all.sh --push # Build and push all Docker containers into DockerHub
./scripts/do_all.sh --pull # Pull all containers from DockerHub with Singularity

Building your own

Most of the containers are designed using Bioconda. The environment.yml file can easilly be modified if particular versions of tools are more suited to your needs. You can then use the building script to build your own containers. You'll just need to specify the correct repository either in command line or in the configuration files.