tools_containers.md

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 1.17.0	Dockerfile	pbmm2@sha256:5f3f4d1f5dbea5cd4c388ee26b2fecbbb7dbcef449343633e039dca3d3725859
mosdepth	mosdepth 0.3.9	Dockerfile	mosdepth@sha256:63f7a5d1a4a17b71e66d755d3301a951e50f6b63777d34dab3ee9e182fd7acb1
sawfish	sawfish 2.0.3 sawshark 0.3.0	Dockerfile	sawfish@sha256:561b6a232dd89a2d186b19d6ad439c74c460078348dbf96ae49ca0ea6eab0281
trgt	trgt 3.0.0 /opt/scripts/check_trgt_coverage.py 0.1.0	Dockerfile	trgt@sha256:301fd3f8c0174213e82dbf942e6f2259aab31a66a7dc3355a3dfc8fcd4286284
hiphase	hiphase 1.5.0	Dockerfile	hiphase@sha256:353b4ffdae4281bdd5daf5a73ea3bb26ea742ef2c36e9980cb1f1ed524a07482
mitorsaw	mitorsaw 0.2.3	Dockerfile	mitorsaw@sha256:4a1eac52a6ae80b7ccfb0ad3809f5f34a69c7ed859541e097e36d73623e8ad0e
paraphase	paraphase 3.3.2 minimap 2.28	Dockerfile	paraphase@sha256:e2f904111a43e8f055681112294e0f05ff2839d9801fc01ac39a17c841016920
pbstarphase	pbstarphase 1.4.1 Database 20250515	Dockerfile	pbstarphase@sha256:7daaad3b617a3b8b5914ab0893ee7cc545fd2025a35619211a5b8e25e4c36ac4
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 1.9.0		deepvariant:1.9.0
deepvariant-gpu	DeepVariant 1.9.0		deepvariant:1.9.0-gpu
pharmcat	PharmCat 2.15.4		pharmcat:2.15.4
glnexus	GLnexus 1.4.3		glnexus:1.4.3