fix: quote env() outputs in RASTAIR_MBIASPARSER for Nextflow strict parser#618
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Bare `env(trim_OT)`/`env(trim_OB)` output declarations fail Nextflow's strict
config/script parser (>=25.10) with "`trim_OT` is not defined". Quote them as
`env('trim_OT')`/`env('trim_OB')`.
Applied as a local nf-core module patch (rastair-mbiasparser.diff) since rastair
is an nf-core/modules-managed module; the same one-line fix will be upstreamed to
nf-core/modules. This was the pipeline's only strict-parser error, so `nextflow
lint` is now clean.
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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. |
mashehu
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Jul 20, 2026
FelixKrueger
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Jul 20, 2026
Brings in dev's rastair strict-parser fix (#618, clears the pre-commit check) and Trim Galore 2.3.0 (#617). The 8 pipeline snapshots are resolved to the template-branch versions here as placeholders; they are regenerated in the following commit against the merged modules (multiqc 1.34 + Trim Galore 2.3.0), since neither branch's snapshots match the merged combination.
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Description
Fixes the Nextflow strict config/script parser (≥25.10) error in
RASTAIR_MBIASPARSER. The bare identifierenv()output declarations:tuple val(meta), env(trim_OT), env(trim_OB), emit: mbias_processed_strfail the strict parser with
`trim_OT` is not defined/`trim_OB` is not defined. The strict parser requires quoted string literals:This was the pipeline's only strict-parser error, so
nextflow lintis now clean — a prerequisite for adopting Nextflow ≥25.10.rastairis an nf-core/modules-managed module, so the change is carried as a local module patch (modules/nf-core/rastair/mbiasparser/rastair-mbiasparser.diff, registered inmodules.json). The same one-line fix is being upstreamed to nf-core/modules; once released, the patch dissolves on the nextnf-core modules update.Verification
nextflow lint→ 0 errors (whole pipeline strict-clean).nf-core modules lint rastair/mbiasparser→ 0 failures (patch registered, somodules_unchangedpasses).PR checklist
CHANGELOG.mdis updated.nextflow lint,nf-core modules lint).Upstream status
The equivalent fix already exists on nf-core/modules
master, bundled into a larger modernization ofrastair/mbiasparser(env vars quoted + renamed toTRIM_OT/TRIM_OB, container apptainer support, and a migration to topic-channel versions). Because adopting that wholesale vianf-core modules updatewould also pull the topic-versions API change (emit: versions→topic: versions) and require rewiringbam_taps_conversion, this PR keeps the minimal local patch for now. The patch will dissolve when the rastair modules are updated to topic-versions in a separate task — so no upstream PR is needed.