docs: add missing PyPOLCA citations#1076
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PyPOLCA was added as an optional long-read assembly polisher (nf-core#1048) but was not cited anywhere. Add it to: - README.md pipeline tool list - CITATIONS.md - toolCitationText() and toolBibliographyText() in the pipeline utils subworkflow, gated on params.run_pypolca, so the auto-generated methods description and bibliography include it when the tool is run. Citation: Bouras et al. (2024), doi: 10.1099/mgen.0.001254. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
dialvarezs
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d4straub,
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muabnezor and
prototaxites
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July 15, 2026 07:06
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
mashehu
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Jul 15, 2026
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PyPOLCA was added as an optional short-read polisher for long-read assemblies in #1048, but its citation was never added.
This PR adds PyPOLCA to the three places a tool citation belongs:
README.md— pipeline tool list.CITATIONS.md— full reference (Bouras et al. 2024, doi: 10.1099/mgen.0.001254).subworkflows/local/utils_nfcore_mag_pipeline/main.nf—toolCitationText()andtoolBibliographyText(), gated onparams.run_pypolca, so the auto-generated methods description and bibliography include PyPOLCA when the tool is run.PR checklist
nf-core pipelines lint).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).🤖 Generated with Claude Code