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 | 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 |
v2.0.4 |
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 | 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 | t1k | T1K_IMAGE |
quay.io/biocontainers/t1k |
1.0.10--h5814d7d_0 |
|
| 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) |
| Sample identity and contamination (step 33) | somalier | SOMALIER_IMAGE |
quay.io/biocontainers/somalier |
0.3.5--h5205c93_0 |
|
| Sample identity and contamination (step 33) | verifybamid2 | VERIFYBAMID2_IMAGE |
quay.io/biocontainers/verifybamid2 |
2.0.3--hc004090_0 |
|
| 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:3.14.8 |
sha256:1eb6b7d4b76454b1de8317863ac3213b678c337b27e604a4e3fb70bddbb2bad7 |
patch tag pinned to its digest: the publisher rebuilds 3.14.8 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 |
|
| 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 |