Genetic map samplesheet validation rejects non-standard chromosome names
@LouisLeNezet is already working on this.
Since Aug 21, 2026.
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Description
Description of feature
Hi everyone, thanks for this awesome nf-core pipeline :)
I'm trying to include a genetic map in the workflow, but I'm working with unconventional chromosomes name (e.g., NC_044187.1 instead of chr1/1).
I'm getting the following error:
Error for field 'chr' (NC_044187.1): "NC_044187.1" does not match regular expression [^(chr)?[0-9]+
$] (Chromosome must be provided and must be a string containing only numbers, with or without the prefix 'chr')
The panel samplesheet already accepts unconventional chromosome names without issues, so it seems inconsistent that the genetic map samplesheet validation is more restrictive.
Is there an easy workaround for this? I'd rather avoid renaming chromosomes across all VCF files if possible.
I've attached a genetic map samplesheet and an example map file for one chromosome for reference.
genetic_map_samplesheet_ex.csv
Suggested enhancement
Relax the chromosome name validation in the genetic map samplesheet, with same logic as in the panel samplesheet, which already handles non-standard NCBI-style names correctly.
Thanks in advance,
Alessio
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