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See https://nfcore.slack.com/archives/C04QR0T3G3H/p1770036127541799: We pushed a patch-release for nf-core tools (3.5.2) without any template changes. Unfortunately, this still results in the outdated comment being added to your PRs, e.g., nf-core/mag#970 (comment). Sorry, for that. Either ignore them or just update the nf-core version in .nf-core.yml to 3.5.2
Add missing visium hd file checks
Co-authored-by: Christophe Avenel <christophe.avenel@it.uu.se>
Co-authored-by: Christophe Avenel <christophe.avenel@it.uu.se>
Co-authored-by: Christophe Avenel <christophe.avenel@it.uu.se>
Co-authored-by: Christophe Avenel <christophe.avenel@it.uu.se>
Local module updates
Use `merge="same"` for the `ADATA_MERGE` module and remove the `add_var` function, instead just drop per-sample annotations that are not useful for the merged object (i.e. for downstream integration).
The integration step was previously run on the per-sample PCAs, which was wrong. Now, perform pre-processing of the merged AnnData before integration, meaning normalisation, log-transformation, HVG selection and a new PCA.
Add the `basis` variable to HARMONY and SCANORAMA modules instead of hard-coding `"X_pca"`.
Move QC metric calculation and filtering out of the PREPROCESSING subworkflow, so that it can be used both for the per-sample and integration branches.
Integration fix
Move seqeralabs/action-tower-launch to @v2 (v2.4.0)
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❌ nf-test failed with latest Nextflow versionNote Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
See the full run for details. |
Skitionek
changed the base branch from
template-merge-158
to
nf-core-template-merge-4.2.1
November 1, 2026 19:31
Nextflow reports tool versions in insertion order on 25.10.4 and alphabetically on newer releases, so a snapshot recorded under one order fails under the other. The pipeline-level tests failed on the pinned 25.10.4 while latest-everything passed. Sorting the keys of every leaf dict in the snapshots makes them match whichever order ran them. Values are untouched: all 35 files differ only in key order. This is nf-migrate's SnapNormalize operation, which landed after this branch was generated.
SnapNormalize sorted every dict whose values were not dicts, which reordered the nft-anndata obs/var summaries. nf-test compares those verbatim, so all nf-test shards failed on an index/columns mismatch. Only the tool-to-version maps are sorted now.
Skitionek
added a commit
to Skitionek/nf-migrate
that referenced
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Nov 1, 2026
SnapNormalize sorted every dict whose values were not dicts. The nft-anndata obs/var summaries qualify, so it reordered them and moved "index" after "columns". nf-test compares those verbatim, which failed every nf-test shard on nf-core/spatialvi#160. A dict is now sorted only when all its values are strings, which is true of the tool-to-version maps and of nothing else in a snapshot. The nf-test "meta" block is left alone as well.
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Migration of template sync PR #158 applied with nf-migrate. No conflicts remain. Stacked on top of the merge PR.