Fix sample name mangling in tximport #9407
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Addresses nf-core/rnaseq#1445 R's data.frame() function automatically modifies column names when check.names=TRUE (the default), which causes issues with sample names that: - Start with numbers (prepends "X": "1A2" -> "X1A2") - Contain special characters like hyphens (converts to dots: "D10-D" -> "D10.D") This caused the downstream summarizedexperiment script to fail when trying to match sample IDs from count matrices against the samplesheet metadata, as the names no longer matched. PR #6638 partially fixed this issue by adding check.names=FALSE to the build_table() function, but missed three additional data.frame() and read.csv() calls that also needed this parameter. This commit adds check.names=FALSE to: 1. Line 76: read.csv() when reading transcript info 2. Line 79: data.frame() when creating extra transcript info rows 3. Line 134: data.frame() when creating coldata (the main bug) The coldata fix (line 134) is the most critical as it directly affects sample names that become column names in the output matrices.
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Thanks @JoseEspinosa ! |
SPPearce
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Nov 14, 2025
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Is this actually going to fix the problem downstream?
Any other R package used is likely to fail in this manner.
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I've already spent some time nobbling other instances, hoping this will catch the remainder |
This was referenced Nov 14, 2025
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Description
Fixes nf-core/rnaseq#1445
This PR fixes an issue where R's
data.frame()function was automatically modifying sample names, causing downstream errors when trying to match sample IDs between count matrices and samplesheet metadata.The Problem
R's
data.frame()automatically modifies column/row names whencheck.names=TRUE(the default):1A2→X1A2D10-D→D10.DThis caused the
SUMMARIZEDEXPERIMENTprocess to fail with:Root Cause
While PR #6638 partially fixed this by adding
check.names = FALSEto thebuild_table()function, it missed three additional locations wheredata.frame()andread.csv()calls were made without this parameter.The most critical one was at line 134 where
coldatais created - this directly sets the sample names that become column names in all output matrices.Changes Made
Added
check.names = FALSEto three function calls intximport.r:read.csv()when reading transcript infodata.frame()when creating extra transcript info rowsdata.frame()when creating coldata (main bug fix)Testing
This fix ensures that sample names are preserved exactly as provided in the input, preventing mismatches downstream. Users can now safely use:
1A2,5B2)sample-1,D10-D)PR checklist
nf-test test path/to/test.nf.test)docs/usage.mdis updateddocs/output.mdis updatedCHANGELOG.mdis updatedREADME.mdis updated (including new tool citations and authors/contributors)