tools_containers

Tool versions and Containers

Containers are used to package tools and their dependencies. This ensures that the tools are reproducible and can be run on any system that supports the container runtime. Our containers are built using Docker and are compatible with any container runtime that supports the OCI Image Specification, like Singularity or Podman.

Most of our containers are built on the pb_wdl_base container, which includes common bioinformatics tools and libraries. We tag our containers with a version number and build count, but the containers are referenced within the WDL files by the sha256 sum tags for reproducibility and better compatibility with Cromwell and miniwdl call caching.

Our Dockerfiles can be inspected on GitHub, and the containers can be pulled from our Quay.io organization.

We directly use deepvariant, deepvariant-gpu, pharmcat, and glnexus containers from their respective authors, although we have mirrored some for better compatibility with Cromwell call caching.

Container	Major tool versions	Dockerfile	Container
pb_wdl_base	htslib 1.20 bcftools 1.20 samtools 1.20 bedtools 2.31.0 python3.9 numpy 1.24.24 pandas 2.0.3 matplotlib 3.7.5 seaborn 0.13.2 pysam 0.22.1 vcfpy 0.13.8 biopython 1.83	Dockerfile	sha256:4b889a1f21a6a7fecf18820613cf610103966a93218de772caba126ab70a8e87
pbmm2	pbmm2 1.16.99	Dockerfile	pbmm2@sha256:b58eef0645dd9adca850c9b4811f289ddcd57f630596d9f524701bc787467f30
mosdepth	mosdepth 0.3.9	Dockerfile	mosdepth@sha256:63f7a5d1a4a17b71e66d755d3301a951e50f6b63777d34dab3ee9e182fd7acb1
pbsv	pbsv 2.10.0	Dockerfile	pbsv@sha256:3a8529853c1e214809dcdaacac0079de70d0c037b41b43bb8ba7c3fc5f783e26
trgt	trgt 1.5.1 /opt/scripts/check_trgt_coverage.py 0.1.0	Dockerfile	trgt@sha256:be7e6ef589a31f4de5d2ed4725dfb34b4b23cb9a440577b606e8f7bfee06526b
hiphase	hiphase 1.4.5	Dockerfile	hiphase@sha256:47fe7d42aea6b1b2e6d3c7401bc35a184464c3f647473d0525c00f3c968b40ad
hificnv	hificnv 1.0.1	Dockerfile	hificnv@sha256:c4764a70c8c2028edb1cdb4352997269947c5076ddd1aeaeef6c5076c630304d
paraphase	paraphase 3.2.1 minimap 2.28	Dockerfile	paraphase@sha256:2823f94682498704bd63fc95314095917fc1cb31a62a674e9d951cec469d2f3e
pbstarphase	pbstarphase 1.1.0 Database 20250110	Dockerfile	pbstarphase@sha256:426764fb09eadbc5de8aea2450b5fe55000c1dd7aaa2ea7b0f5438f34ea63e3d
pb-cpg-tools	pb-cpg-tools 3.0.0	Dockerfile	pb-cpg-tools@sha256:afd5468a423fe089f1437d525fdc19c704296f723958739a6fe226caa01fba1c
wgs_tertiary	/opt/scripts/calculate_phrank.py 2.0.0 /opt/scripts/json2ped.py 0.5.0 Last built 2021-09-17: ensembl -> HGNC ensembl -> HPO HGNC -> inheritance HPO DAG	Dockerfile	wgs_tertiary@sha256:410597030e0c85cf16eb27a877d260e7e2824747f5e8b05566a1aaa729d71136
slivar	slivar 0.3.1 /opt/scripts/add_comphet_phase.py 0.1.0	Dockerfile	slivar@sha256:f71a27f756e2d69ec30949cbea97c54abbafde757562a98ef965f21a28aa8eaa
svpack	svpack 54b54db	Dockerfile	svpack@sha256:628e9851e425ed8044a907d33de04043d1ef02d4d2b2667cf2e9a389bb011eba
deepvariant	DeepVariant 1.6.1		deepvariant:1.6.1
deepvariant-gpu	DeepVariant 1.6.1		deepvariant:1.6.1-gpu
pharmcat	PharmCat 2.15.4		pharmcat:2.15.4
glnexus	GLnexus 1.4.3		glnexus:1.4.3