Personal-Genome-Pipeline/versions.env at main · GeiserX/Personal-Genome-Pipeline · GitHub

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# shellcheck shell=bash
# versions.env — Canonical Docker image versions for the Personal Genome Pipeline
# This is the single source of truth for all container image tags.
# setup.sh and validate-setup.sh source this file.
#
# To update a tool version:
#   1. Change the tag here
#   2. Run: ./scripts/setup.sh <genome_dir>  (pulls new images)
#   3. Update the corresponding script if it hardcodes the image reference
#
# Images pinned to :latest have no versioned tags from their publisher.
# These are noted with comments and should be checked periodically.

# --- Core tools ---
MINIMAP2_IMAGE="quay.io/biocontainers/minimap2:2.28--he4a0461_0"
SAMTOOLS_IMAGE="staphb/samtools:1.20"
BCFTOOLS_IMAGE="staphb/bcftools:1.21"
DEEPVARIANT_IMAGE="google/deepvariant:1.6.0"
FASTP_IMAGE="quay.io/biocontainers/fastp:1.3.1--h43da1c4_0"

# --- Structural variant callers ---
MANTA_IMAGE="quay.io/biocontainers/manta:1.6.0--h9ee0642_2"
DELLY_IMAGE="quay.io/biocontainers/delly:1.7.3--hd6466ae_0"
CNVNATOR_IMAGE="quay.io/biocontainers/cnvnator:0.4.1--py312h99c8fb2_11"
GRIDSS_IMAGE="quay.io/biocontainers/gridss:2.13.2--h96c455f_6"
DUPHOLD_IMAGE="brentp/duphold:v0.2.3"
ANNOTSV_IMAGE="getwilds/annotsv:3.4.4"

# --- Variant annotation ---
VEP_IMAGE="ensemblorg/ensembl-vep:release_112.0"
PCGR_IMAGE="sigven/pcgr:2.2.5"

# --- Pharmacogenomics ---
PHARMCAT_IMAGE="pgkb/pharmcat:3.2.0"

# --- Specialized analysis ---
TELOMEREHUNTER_IMAGE="lgalarno/telomerehunter:latest"  # No versioned tags from publisher
HAPLOGREP3_IMAGE="jtb114/haplogrep3:latest"             # No versioned tags from publisher; genepi/haplogrep3 removed from Docker Hub
T1K_IMAGE="quay.io/biocontainers/t1k:1.0.9--h5ca1c30_0"
EXPANSIONHUNTER_IMAGE="quay.io/biocontainers/expansionhunter:5.0.0--hc26b3af_5"
GOLEFT_IMAGE="quay.io/biocontainers/goleft:0.2.4--h9ee0642_1"
MOSDEPTH_IMAGE="quay.io/biocontainers/mosdepth:0.3.13--hba6dcaf_0"

# --- General purpose ---
GATK_IMAGE="broadinstitute/gatk:4.6.1.0"
PICARD_IMAGE="broadinstitute/picard:3.4.0"
PYTHON_IMAGE="python:3.11"
PLINK2_IMAGE="pgscatalog/plink2:2.00a5.10"
MULTIQC_IMAGE="quay.io/biocontainers/multiqc:1.33--pyhdfd78af_0"

# --- v0.4.0: Annotation enrichment ---
VCFANNO_IMAGE="quay.io/biocontainers/vcfanno:0.3.7--he881be0_0"
# SLIVAR uses staphb/bcftools (BCFTOOLS_IMAGE) + pre-built slivar binary
PYPGX_IMAGE="quay.io/biocontainers/pypgx:0.26.0--pyh7e72e81_0"

# --- Alternative variant callers ---
OCTOPUS_IMAGE="dancooke/octopus:0.7.4"
CLAIR3_IMAGE="hkubal/clair3:v2.0.0"
SNIFFLES_IMAGE="quay.io/biocontainers/sniffles:2.4--pyhdfd78af_0"