containers.md

Containers

Our main container is designed using Conda 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 extra annotation documentation):

• sareksnpeff
• sarekvep

What is actually inside the containers

sarek

• Based on nfcore/base:latest
• Contain ASCAT 2.5.2
• Contain AlleleCount 4.0.2
• Contain BCFTools 1.9
• Contain BWA 0.7.17
• Contain Control-FREEC 11.4
• Contain FastQC 0.11.8
• Contain FreeBayes 1.2.0
• Contain GATK4 4.1.2.0
• Contain GeneSplicer 1.0
• Contain HTSlib 1.9
• Contain Manta 1.5.0
• Contain MultiQC 1.7
• Contain Qualimap 2.2.2b
• Contain samtools 1.9
• Contain snpEff 4.3.1t
• Contain Strelka2 2.9.10
• Contain TIDDIT 2.7.1
• Contain VCFanno 0.3.1
• Contain VCFtools 0.1.16
• Contain VEP 95.2

sareksnpeff

• Based on nfcore/base:latest
• Contain snpEff 4.3.1t
• Contains cache for GRCh37, GRCh38, GRCm38 or CanFam3.1

sarekvep

• Based on nfcore/base:latest
• Contain GeneSplicer 1.0
• Contain VEP 95.2
• Contain cache for GRCh37, GRCh38, GRCm38 or CanFam3.1

Building your own

Our containers are designed using Conda. The environment.yml file can be modified if particular versions of tools are more suited to your needs.

The following commands can be used to build/download containers on your own system:

• Adjust VERSION for sarek version (typically a release or dev).

Build with Conda

conda env create -f environment.yml

Build with Docker

• sarek

docker build -t nfcore/sarek:<VERSION> .

• sareksnpeff

Adjust arguments for GENOME version and snpEff CACHE_VERSION

docker build -t nfcore/sareksnpeff:<VERSION>.<GENOME> containers/snpeff/. --build-arg GENOME=<GENOME> --build-arg CACHE_VERSION=<CACHE_VERSION>

• sarekvep

Adjust arguments for GENOME version, SPECIES name and VEP VEP_VERSION

docker build -t nfcore/sarekvep:<VERSION>.<GENOME> containers/vep/. --build-arg GENOME=<GENOME> --build-arg SPECIES=<SPECIES> --build-arg VEP_VERSION=<VEP_VERSION>

Pull with Docker

• sarek

docker pull nfcore/sarek:<VERSION>

• sareksnpeff

Adjust arguments for GENOME version

docker pull nfcore/sareksnpeff:<VERSION>.<GENOME>

• sarekvep

Adjust arguments for GENOME version

docker pull nfcore/sarekvep:<VERSION>.<GENOME>

Pull with Singularity

You can directly pull singularity image, in the path used by the Nextflow ENV variable NXF_SINGULARITY_CACHEDIR, ie:

cd $NXF_SINGULARITY_CACHEDIR
singularity build ...

• sarek

singularity build nfcore-sarek-<VERSION>.img docker://nfcore/sarek:<VERSION>

• sareksnpeff

Adjust arguments for GENOME version

singularity build nfcore-sareksnpeff-<VERSION>.<GENOME>.img docker://nfcore/sareksnpeff:<VERSION>.<GENOME>

• sarekvep

Adjust arguments for GENOME version

singularity build nfcore-sarekvep-<VERSION>.<GENOME>.img docker://nfcore/sarekvep:<VERSION>.<GENOME>