fix: prevent markers.csv duplication in multi-sample runs (#165) - #166
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fix: prevent markers.csv duplication in multi-sample runs (#165)#166adamjtaylor wants to merge 2 commits into
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… runs (nf-core#165) Multi-sample runs failed in MCQUANT with "number of channels in markers.csv doesn't match the image" whenever samples differed in a per-sample field. Two independent causes, both fixed here: - The shared markersheet was deduplicated with `.unique()` on the whole marker map, which includes per-sample fields (exposure_time/_unit). Any difference left duplicate rows, inflating markers.csv beyond the image channel count. Now rows are grouped by (cycle_number, channel_number) and collapsed to one shared row per channel; samples may differ in exposure (validated separately for backsub), but must agree on the marker definition. - The per-cycle channel offset uniqued (cycle_number, channel_count) pairs, so samples disagreeing on a cycle's channel count silently produced duplicate offsets and duplicated markers. This is now a clear, actionable error. Adds a defense-in-depth assertion that the final markers.csv has exactly one contiguously numbered row (1..N) per image channel. Also removes the previous inter-sample/backsub checks, which operated on the whole list rather than individual rows and never fired. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…ore#165) Two nf-test cases exercising the multi-sample paths that previously produced a malformed markers.csv: - samples differing in exposure time must collapse to one row per image channel (regression against the 44 -> 64 row duplication) - samples disagreeing on a cycle's channel count must fail with a clear error Both feed small committed OME-XML fixtures straight to the xml input so they run OMEVALIDATION natively without a container. The existing single-sample snapshot is unchanged. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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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 Synchronisation documentation. |
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Fixes #165.
markers.csvwith duplicate rows (44 → 64 in the reported case), causing MCQUANT to abort with "number of channels doesn't match".UPDATE_FROM_OMEnow groups markers by(cycle_number, channel_number)and collapses to one row per image channel, instead of.unique()over whole maps that still carried per-sampleexposure_time.1..N, and removed the previous list-level guards that never fired.🤖 Generated with Claude Code