Image versions¶
Every container image the pipeline runs, as pinned in versions.env. The step scripts read the variable named here, and the commands on the step pages use the same variable, for example "${BCFTOOLS_IMAGE}" after source versions.env in the repository root.
This page is generated by scripts/ci/gen-versions-doc.sh from versions.env and the scripts; edit versions.env and rerun the script instead of editing this page. The note column is the comment on that line of versions.env. The Nextflow modules take the same tags from conf/containers.config, which scripts/ci/gen-containers-config.sh writes from versions.env; CI fails when that file is stale.
| Group | Tool | Variable | Image | Pinned version | Note |
|---|---|---|---|---|---|
| Core tools | minimap2 | MINIMAP2_IMAGE |
quay.io/biocontainers/minimap2 |
2.31--h118bc1c_0 |
|
| Core tools | samtools | SAMTOOLS_IMAGE |
staphb/samtools |
1.24 |
|
| Core tools | mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4 | MINIMAP2_SAMTOOLS_IMAGE |
quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4 |
ad4c240457048f1d3cc0bd8c8fa39bf27d222eb7-0 |
hold: minimap2=2.31,samtools=1.24, the releases of MINIMAP2_IMAGE and SAMTOOLS_IMAGE; Nextflow alignment only |
| Core tools | samtools | SAMTOOLS_HTTPS_IMAGE |
quay.io/biocontainers/samtools |
1.25--h9dcdb79_0 |
optional: docs/quick-test.md reads a CRAM over https with it; SAMTOOLS_IMAGE has no CA certificates |
| Core tools | bcftools | BCFTOOLS_IMAGE |
staphb/bcftools |
1.24 |
|
| Core tools | deepvariant | DEEPVARIANT_IMAGE |
google/deepvariant |
1.10.0 |
|
| Core tools | fastp | FASTP_IMAGE |
quay.io/biocontainers/fastp |
1.4.0--h43da1c4_0 |
|
| Alternative aligners and callers (optional) | bwa-mem2 | BWAMEM2_IMAGE |
quay.io/biocontainers/bwa-mem2 |
2.3--he70b90d_0 |
optional: step 02a; 2.3 reads a 2.2.1 index (no index code changed between the two) |
| Alternative aligners and callers (optional) | bwa | BWA_IMAGE |
quay.io/biocontainers/bwa |
0.7.19--h577a1d6_1 |
optional: classic BWA index for GRIDSS (step 04b) |
| Alternative aligners and callers (optional) | freebayes | FREEBAYES_IMAGE |
quay.io/biocontainers/freebayes |
1.3.10--h3752d28_1 |
optional: step 03b |
| Alternative aligners and callers (optional) | strelka | STRELKA_IMAGE |
quay.io/biocontainers/strelka |
2.9.10--h9ee0642_1 |
optional: step 03c; legacy: no automated bumps |
| Alternative aligners and callers (optional) | octopus | OCTOPUS_IMAGE |
dancooke/octopus |
0.7.4 |
optional: step 03d; legacy: no automated bumps |
| Alternative aligners and callers (optional) | clair3 | CLAIR3_IMAGE |
hkubal/clair3 |
v2.0.5 |
optional: step 03e |
| Alternative aligners and callers (optional) | tiddit | TIDDIT_IMAGE |
quay.io/biocontainers/tiddit |
3.9.7--py312hfcd9dac_0 |
optional: step 04a |
| Alternative aligners and callers (optional) | sniffles | SNIFFLES_IMAGE |
quay.io/biocontainers/sniffles |
2.8.0--pyhdfd78af_1 |
optional: step 04c; hold: 2.8.1 waits for bioconda |
| Alternative aligners and callers (optional) | hap.py | HAPPY_IMAGE |
jmcdani20/hap.py |
v0.3.12 |
optional: benchmark-variants.sh; the hap.py biocontainer (0.3.15) has no RTG Tools, so it cannot run --engine=vcfeval |
| Structural variant callers | manta | MANTA_IMAGE |
quay.io/biocontainers/manta |
1.6.0--h9ee0642_2 |
legacy: no automated bumps |
| Structural variant callers | delly | DELLY_IMAGE |
quay.io/biocontainers/delly |
2.7.0--h3752d28_0 |
since 2.3.0 the short-read caller is delly sr, not delly call |
| Structural variant callers | cnvpytor | CNVPYTOR_IMAGE |
quay.io/biocontainers/cnvpytor |
1.3.2--pyhdfd78af_0 |
|
| Structural variant callers | gridss | GRIDSS_IMAGE |
quay.io/biocontainers/gridss |
2.13.2--h96c455f_6 |
legacy: no automated bumps |
| Structural variant callers | duphold | DUPHOLD_IMAGE |
brentp/duphold |
v0.2.3 |
legacy: no automated bumps |
| Structural variant callers | annotsv | ANNOTSV_IMAGE |
quay.io/biocontainers/annotsv |
3.5.10--hdfd78af_0 |
|
| Structural variant callers | stranger | STRANGER_IMAGE |
quay.io/biocontainers/stranger |
0.10.2--pyhdfd78af_0 |
|
| Structural variant callers | survivor | SURVIVOR_IMAGE |
quay.io/biocontainers/survivor |
1.0.7--h077b44d_7 |
step 22; legacy: no automated bumps (last release 2019) |
| Variant annotation | ensembl-vep | VEP_IMAGE |
ensemblorg/ensembl-vep |
release_116.3 |
|
| Variant annotation | pcgr | PCGR_IMAGE |
ghcr.io/sigven/pcgr |
2.3.2 |
Docker Hub sigven/pcgr stops at 2.2.5; 2.3.x is on ghcr.io |
| Pharmacogenomics | pharmcat | PHARMCAT_IMAGE |
pgkb/pharmcat |
3.4.0 |
|
| Pharmacogenomics | pypgx | PYPGX_IMAGE |
quay.io/biocontainers/pypgx |
0.26.0--pyh7e72e81_0 |
|
| Specialized analysis | telomerehunter | TELOMEREHUNTER_IMAGE |
quay.io/biocontainers/telomerehunter |
1.1.0--pyhdfd78af_0 |
run with --plotNone: the plots of this build fail (its R lacks dplyr) |
| Specialized analysis | haplogrep3 | HAPLOGREP3_IMAGE |
quay.io/biocontainers/haplogrep3 |
3.2.2--hdfd78af_1 |
|
| Specialized analysis | haplocheck | HAPLOCHECK_IMAGE |
quay.io/biocontainers/haplocheck |
1.3.3--h2a3209d_2 |
step 12: mtDNA contamination; legacy: no automated bumps (last release 2022) |
| Specialized analysis | eklipse | EKLIPSE_IMAGE |
quay.io/biocontainers/eklipse:1.8--hdfd78af_6 |
sha256:edd58aa92dcd62a39328d20b044fc024978afce31f70ba5cd174279f85146705 |
step 20: large mtDNA deletions; upstream has no release: the Bioconda recipe builds commit 3606cb2edac983d2623ddc667b49206c3d01373c (2022-02-03), AGPL-3.0, run as its own tool; legacy: no automated bumps (eKLIPse is no longer maintained) |
| Specialized analysis | yleaf | YLEAF_IMAGE |
quay.io/biocontainers/yleaf |
3.2.1--pyh1286868_0 |
optional: step 37 (opt-in); hold: the only biocontainer, upstream is 4.x |
| Specialized analysis | hipstr | HIPSTR_IMAGE |
quay.io/biocontainers/hipstr |
0.7--hcf09f9e_1 |
optional: step 45 (opt-in, Y-STR repeat counts of male samples) |
| Specialized analysis | t1k | T1K_IMAGE |
quay.io/biocontainers/t1k |
1.0.10--h5814d7d_0 |
|
| Specialized analysis | optitype | OPTITYPE_IMAGE |
quay.io/biocontainers/optitype |
1.5.0--pyhdfd78af_1 |
optional: step 08 with HLA_QC=true (opt-in second HLA caller, class I) |
| Specialized analysis | expansionhunter | EXPANSIONHUNTER_IMAGE |
quay.io/biocontainers/expansionhunter |
5.0.0--hc26b3af_5 |
|
| Specialized analysis | goleft | GOLEFT_IMAGE |
quay.io/biocontainers/goleft |
0.2.6--he881be0_1 |
|
| Specialized analysis | mosdepth | MOSDEPTH_IMAGE |
quay.io/biocontainers/mosdepth |
0.3.14--h87be163_2 |
|
| Specialized analysis | parascopy | PARASCOPY_IMAGE |
quay.io/biocontainers/parascopy |
1.19.0--py311h98bf483_0 |
optional: step 35 (opt-in, SMN1/SMN2 copy number) |
| Specialized analysis | paraphase | PARAPHASE_IMAGE |
quay.io/biocontainers/paraphase |
4.1.0--h9ee0642_0 |
optional: step 35b (opt-in, PacBio HiFi BAMs only: its licence allows PacBio data only) |
| Specialized analysis | megane | MEGANE_IMAGE |
shoheikojima/megane:v1.0.1.beta |
sha256:f7d38cc1a4f41797d84214e326336bbbeebd3f20ffca8416308ecc48143c6b10 |
optional: step 50 (opt-in, Alu, L1 and SVA insertions) |
| Specialized analysis | vntyper | VNTYPER_IMAGE |
ghcr.io/hassansaei/vntyper |
2.0.47 |
optional: step 52 (opt-in, MUC1 VNTR frameshifts); the publisher's image, reference data inside, about 3 GB (Docker Hub's saei/vntyper stops at 2.0.3) |
| Sample identity and contamination (step 33) | somalier | SOMALIER_IMAGE |
quay.io/biocontainers/somalier |
0.3.6--h5205c93_0 |
|
| Sample identity and contamination (step 33) | verifybamid2 | VERIFYBAMID2_IMAGE |
quay.io/biocontainers/verifybamid2 |
2.0.3--hc004090_0 |
|
| Family analysis (step 38, opt-in: a pedigree of two or more samples) | glnexus | GLNEXUS_IMAGE |
quay.io/biocontainers/glnexus |
1.4.1--h17e8430_5 |
optional: step 38, the joint call of the members' gVCFs |
| Family analysis (step 38, opt-in: a pedigree of two or more samples) | whatshap | WHATSHAP_IMAGE |
quay.io/biocontainers/whatshap |
2.8--py312hf731ba3_0 |
step 42, read-backed phasing of the genotype rules that need it; step 38, phasing by inheritance (whatshap phase --ped) |
| Family analysis (step 38, opt-in: a pedigree of two or more samples) | hap-ibd | HAP_IBD_IMAGE |
quay.io/biocontainers/hap-ibd |
1.0.rev20May22.818--hdfd78af_0 |
optional: step 38, shared segments between members (with BEAGLE_IMAGE and step 26b's panel) |
| Symptom-driven ranking (step 48, opt-in: HPO terms) | exomiser-cli | EXOMISER_IMAGE |
exomiser/exomiser-cli |
15.1.0-bash |
optional: step 48 (opt-in, runs with HPO terms) |
| General purpose | gatk | GATK_IMAGE |
broadinstitute/gatk |
4.7.0.0 |
|
| General purpose | picard | PICARD_IMAGE |
broadinstitute/picard |
3.5.0 |
|
| General purpose | python | PYTHON_IMAGE |
python:3.15.2 |
sha256:d7a732b20de2f5d3cf977cbcf69aacf30dc928a37908ff9fdb7bb3503024c91a |
patch tag pinned to its digest: the publisher rebuilds a patch tag in place |
| General purpose | plink2 | PLINK2_IMAGE |
pgscatalog/plink2 |
2.00a5.10 |
|
| Polygenic scores and ancestry (steps 25 and 26) | pygscatalog | PGSC_UTILS_IMAGE |
ghcr.io/pgscatalog/pygscatalog |
pgscatalog-utils-2.0.4 |
|
| Polygenic scores and ancestry (steps 25 and 26) | fraposa_pgsc | PGSC_FRAPOSA_IMAGE |
ghcr.io/pgscatalog/fraposa_pgsc |
v1.0.2 |
|
| Polygenic scores and ancestry (steps 25 and 26) | pyyaml | PGSC_PYYAML_IMAGE |
ghcr.io/pgscatalog/pyyaml |
6.0 |
|
| Polygenic scores and ancestry (steps 25 and 26) | zstd | PGSC_ZSTD_IMAGE |
ghcr.io/pgscatalog/zstd:2-beta |
sha256:dea95df4f1bdee59190e5e4b88112d7f7b461463550c47d4e1c1f2526b6bd442 |
|
| Polygenic scores and ancestry (steps 25 and 26) | report | PGSC_REPORT_IMAGE |
ghcr.io/pgscatalog/report:2-beta |
sha256:6d1ba573648346a0ae3f24418a898d202a8c581d5d190f83baa8d0db13ee02be |
|
| Polygenic scores and ancestry (steps 25 and 26) | multiqc | MULTIQC_IMAGE |
quay.io/biocontainers/multiqc |
1.35--pyhdfd78af_2 |
|
| Fine-grained ancestry (step 26b, opt-in) | admixture | ADMIXTURE_IMAGE |
quay.io/biocontainers/admixture |
1.3.0--0 |
optional: step 26b; legacy: no automated bumps (1.3.0 is the only BioContainers build) |
| Fine-grained ancestry (step 26b, opt-in) | beagle | BEAGLE_IMAGE |
quay.io/biocontainers/beagle |
5.5_27Feb25.75f--hdfd78af_0 |
optional: steps 26b and 51 phasing |
| Fine-grained ancestry (step 26b, opt-in) | rfmix | RFMIX_IMAGE |
quay.io/biocontainers/rfmix |
2.03.r0.9505bfa--h503566f_8 |
optional: step 26b painting; legacy: no automated bumps (last release 2017) |
| Fine-grained ancestry (step 26b, opt-in) | bcftools | BCFTOOLS_HTTPS_IMAGE |
quay.io/biocontainers/bcftools |
1.25--h118bc1c_1 |
optional: setup.sh --ancestry-fine-panel reads the panel over https; BCFTOOLS_IMAGE has no CA certificates |
| Mosaic chromosomal alterations (step 51, opt-in) | bcftools | MOCHA_IMAGE |
us.gcr.io/mccarroll-mocha/bcftools:1.22-20250819 |
sha256:c9398385cfe3a968918ddf470e2769b7ee42cbc0bb8f564b4744c460343550a5 |
optional: step 51; hold: tag and digest move with MOCHA_COMMIT |
| Archaic ancestry (step 43, opt-in) | ibdmix | IBDMIX_IMAGE |
quay.io/biocontainers/ibdmix |
1.0.1--h4ac6f70_2 |
optional: step 43; legacy: no automated bumps (1.0.1, 2022, is the last release) |
| Ancient populations (step 44, opt-in) | eigensoft | EIGENSOFT_IMAGE |
quay.io/biocontainers/eigensoft |
9.0.0--h519d32d_0 |
optional: step 44 |
| Annotation enrichment | vcfanno | VCFANNO_IMAGE |
quay.io/biocontainers/vcfanno |
0.3.9--h1079eea_0 |
|
| Annotation enrichment | slivar | SLIVAR_IMAGE |
quay.io/biocontainers/slivar |
0.3.4--hb56abc1_0 |