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Update Clair3, ClairS, DeepVariant and DeepSomatic #213
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Merged
AmberVerhasselt
merged 8 commits into
chore/module-updates
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chore/variant-caller-updates
Oct 2, 2026
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0e628ff
Update Clair3, ClairS, DeepVariant and DeepSomatic
ljwharbers 7cb08bb
Restore DeepVariant edits that were missing from the patch files
ljwharbers c1d0489
Update default, chm13 and clair_only snapshots for the new callers
ljwharbers 69ebae2
Update consensus, deep_only and union snapshots for the new callers
ljwharbers d3d4614
Fill in PR number in CHANGELOG entry
ljwharbers 906aad3
Skip nf-core component tests in nextflow-lint
ljwharbers a8d27e6
Merge branch 'chore/module-updates' into chore/variant-caller-updates
ljwharbers fc0e823
Address review: DeepSomatic small model, ClairS container ternary
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -4,4 +4,4 @@ channels: | |
| - conda-forge | ||
| - bioconda | ||
| dependencies: | ||
| - "bioconda::clair3=1.0.10" | ||
| - "bioconda::clair3=2.0.3" | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| process CLAIR3_MODEL { | ||
| tag "${meta.id}" | ||
| label 'process_single' | ||
|
|
||
| conda "${moduleDir}/environment.yml" | ||
| container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container | ||
| ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3b/3b54fa9135194c72a18d00db6b399c03248103f87e43ca75e4b50d61179994b3/data' | ||
| : 'community.wave.seqera.io/library/wget:1.21.4--8b0fcde81c17be5e'}" | ||
|
|
||
| input: | ||
| tuple val(meta), val(url) | ||
|
|
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| output: | ||
| tuple val(meta), path("${meta.id}", type: 'dir'), emit: model | ||
| tuple val("${task.process}"), val('wget'), eval('wget --version | head -1 | cut -d " " -f 3'), emit: versions_wget, topic: versions | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
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| script: | ||
| def args = task.ext.args ?: '' | ||
| // Clair3 v2 models are directories holding two PyTorch checkpoints, served unpacked | ||
| """ | ||
| mkdir ${meta.id} | ||
| for checkpoint in pileup.pt full_alignment.pt; do | ||
| wget ${args} -O ${meta.id}/\$checkpoint ${url}/\$checkpoint | ||
| done | ||
| """ | ||
|
|
||
| stub: | ||
| """ | ||
| mkdir ${meta.id} | ||
| touch ${meta.id}/pileup.pt ${meta.id}/full_alignment.pt | ||
| """ | ||
| } |
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No PR-CI coverage for the DeepVariant/DeepSomatic changes. PR CI only runs tests tagged
small, and onlytests/default.nf.testhas that tag. It runs withgermline_var_keep = 'clair'andsomatic_var_keep = 'clair', and its snapshot has noDEEPVARIANT_*/DEEPSOMATIC_*entries. That leaves several changes without CI coverage: the 1.10 image bump, the new--checkpoint-driven make_examples flags here and at L208, the rebuilt DeepVariant patches (including the${meta.id}_germlineprefix), and the newgzi/with_phasingsubworkflow arguments. Only theextendedtests (deep_only, consensus, union, chm13) exercise them. Please run the Slurm test array and link the results before merge.There was a problem hiding this comment.
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Ran the Slurm array on fc0e823 (this head, with #212 merged in) on Mindwell,
-profile debug,test,apptainer --update-snapshot, job 11645738. All seven pass: default, clair_only, consensus, deep_only, union, chm13 and the tumour-only subworkflow test.git statuswas clean afterwards, so no snapshot moved with the review changes.The DeepVariant/DeepSomatic outputs hold real calls, not empty files (records / PASS):
The deep_only and union counts are identical. The few somatic PASS calls are expected on the small chr subsets.
The real-data C8 comparison found a bcftools 1.24 problem in #212 (see the PR description and #212). It's fixed and resubmitted as Slurm 11645745. I'll post the caller comparison here when it finishes.