fix: address remaining PR #176 review comments - #187
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ljwharbers merged 1 commit intoSep 2, 2026
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Two nits from the Copilot review threads on #176 that were still real: - README: "a `multiqc` report from that combines" dropped the stray "from", and "one html report" -> "one HTML report". - LRSOMATICREPORT: quote the interpolated paths in the script block. The `Rscript` invocation passed report_src, the sample id, the sex and the output filename unquoted, so a projectDir or sample id containing a space would word-split; the flat-input symlink loop had the same shape. ${args} stays unquoted -- it is a pre-built argument string that already quotes each `--gene-panel` value in conf/modules.config. No output or version changes, so no snapshots move. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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ljwharbers
merged commit Sep 2, 2026
3d454bf
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worktree-lrsomatic-report-module
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Summary
Closes out the two review threads on #176 that still pointed at something real in the code. Everything else open on that PR was either already fixed (the threads just never got resolved) or factually wrong — see the audit note posted on #176.
README.md:107— "amultiqcreport from that combines the output frommosdepthandsamtoolsinto one html report" → drops the stray "from" and capitalises HTML. Flagged three times on Add LRSOMATICREPORT as the final pipeline step #176 (r3880745421, plus twice as a suppressed comment).modules/local/lrsomaticreport/main.nf— quote the interpolated paths in the script block (r3880745383). TheRscriptinvocation passedreport_src, the sample id, the sex and the output filename unquoted, so aprojectDiror sample id containing a space would word-split; the flat-input symlink loop had the same shape.${args}deliberately stays unquoted — it is a pre-built argument string, and each--gene-panelvalue is already quoted where it is assembled inconf/modules.config.Test plan
nextflow lint modules/local/lrsomaticreport/main.nf— cleanpre-commit run --files README.md modules/local/lrsomaticreport/main.nf— cleannf-test test modules/local/lrsomaticreport/tests/main.nf.test --profile singularity— all 4 tests pass (stub, real render, gene-panel render, multi-panel render), no snapshot changesThe real-render test asserts the rendered HTML contains
TP53, which can only get there through thelink_flatsymlink loop, so the quoted loop is verified end to end rather than just parsed.🤖 Generated with Claude Code