Our main container is designed using Conda to install all tools used in 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):
- 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 11.5
- Contain FastQC 0.11.8
- Contain FreeBayes 1.3.1
- Contain GATK4 4.1.4.0
- Contain GeneSplicer 1.0
- Contain HTSlib 1.9
- Contain Manta 1.6.0
- Contain MultiQC 1.7
- Contain Qualimap 2.2.2c
- Contain samtools 1.9
- Contain snpEff 4.3.1t
- Contain Strelka2 2.9.10
- Contain TIDDIT 2.8.0
- Contain VCFanno 0.3.2
- Contain VCFtools 0.1.16
- Contain VEP 98.2
- Based on
nfcore/base:latest - Contain snpEff 4.3.1t
- Contains cache for
GRCh37,GRCh38,GRCm38orCanFam3.1
- Based on
nfcore/base:latest - Contain GeneSplicer 1.0
- Contain VEP 98.2
- Contain cache for
GRCh37,GRCh38,GRCm38orCanFam3.1
A helper script, used for testing can also be used to help with pulling docker containers, or building singularity images. The following parameters can be used:
Specify which container engine to use: docker or singularity.
Default:docker
Specify which containers to build: SNPEFF, VEP or ALL.
Default:ALL
Specify which release to pull or build: any tagged release, or dev.
Default:dev
Specify which release genome to use for annotation containers (sareksnpeff, sarekvep): smallGRCh37, GRCh37, GRCh38, GRCm38 or CanFam3.1.
Default:smallGRCh37
To specify where to build singularity image, use the Nextflow ENV variable NXF_SINGULARITY_CACHEDIR, ie:
NXF_SINGULARITY_CACHEDIR=/data/singularity ./scripts/download_image.sh -n singularity -t ALL -T dev -g GRCh38That will build the main container, plus the annotation containers (sareksnpeff, sarekvep) for GRCh38, in the /data/singularity folder.
Our containers are designed using Conda.
The environment.yml file can easilly be modified if particular versions of tools are more suited to your needs.