Update Bismark to 3.1.0#614
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Update the 7 bismark modules from 3.0.0 to 3.1.0 (nf-core/modules#12356): containers, environment.yml, meta.yml containers block and per-arch conda-lock files, plus the modules.json shas. Bismark 3.1.0 is a byte-identical drop-in for 3.0.0 on the standard path, so the pipeline nf-test snapshots only change the reported bismark version (3.0.0 -> 3.1.0).
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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CI is fully green ✅ — the full-pipeline nf-tests (docker + singularity, all shards) pass with only the reported cc @pinin4fjords 🙏 |
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Update Bismark to 3.1.0
Bumps the 7 bismark nf-core modules from 3.0.0 → 3.1.0, following nf-core/modules#12356 (merged).
Bismark 3.1.0 is a byte-identical drop-in for 3.0.0 on the standard bisulfite path — the module-level nf-tests in nf-core/modules#12356 passed with only the reported version string changed — so this is a version/container currency bump with no change to results.
Changes
nf-core modules updateforalign,coverage2cytosine,deduplicate,genomepreparation,methylationextractor,report,summary— containers → the 3.1.0 Seqera images (+ per-arch conda-locks +meta.ymlcontainers block);modules.jsonshas →7d264419."bismark"version3.0.0→3.1.0(outputs byte-identical).Note
Draft while CI runs: if the full-pipeline nf-tests flag md5 changes (e.g. a MultiQC report embedding the version string), the affected snapshots will need a native regen — I couldn't run the full pipeline tests locally (amd64 emulation). CI will confirm.
cc @pinin4fjords — follow-up to the 3.0.0 bump (#610).