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 1.16.0	Dockerfile	pbmm2@sha256:24218cb5cbc68d1fd64db14a9dc38263d3d931c74aca872c998d12ef43020ef0
mosdepth	mosdepth 0.3.9	Dockerfile	mosdepth@sha256:63f7a5d1a4a17b71e66d755d3301a951e50f6b63777d34dab3ee9e182fd7acb1
pbsv	pbsv 2.10.0	Dockerfile	pbsv@sha256:3a8529853c1e214809dcdaacac0079de70d0c037b41b43bb8ba7c3fc5f783e26
trgt	trgt 1.2.0 /opt/scripts/check_trgt_coverage.py 0.1.0	Dockerfile	trgt@sha256:0284ff5756f8d47d9d81b515b8b1a6c81fac862ae5a7b4fe89f65235c3e5e0c9
hiphase	hiphase 1.4.5	Dockerfile	hiphase@sha256:47fe7d42aea6b1b2e6d3c7401bc35a184464c3f647473d0525c00f3c968b40ad
hificnv	hificnv 1.0.1	Dockerfile	hificnv@sha256:c4764a70c8c2028edb1cdb4352997269947c5076ddd1aeaeef6c5076c630304d
paraphase	paraphase 3.1.1 minimap 2.28	Dockerfile	paraphase@sha256:a114ac5b9a682d7dc0fdf25c92cfb36f80c07ab4f1fb76b2e58092521b123a4d
pbstarphase	pbstarphase 1.0.0 Database 20240826	Dockerfile	pbstarphase@sha256:6954d6f7e462c9cec7aaf7ebb66efaf13d448239aab76a3c947c1dfe24859686
pb-cpg-tools	pb-cpg-tools 2.3.2	Dockerfile	pb-cpg-tools@sha256:d6e63fe3f6855cfe60f573de1ca85fab27f4a68e24a7f5691a7a805a22af292d
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@sha256:35be557730d3ac9e883f1c2010fb24ac02631922f9b4948b0608d3e643a46e8b
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