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Update geneticmapconvert - #12852

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LouisLeNezet:geneticmap
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Update geneticmapconvert#12852
LouisLeNezet wants to merge 2 commits into
nf-core:masterfrom
LouisLeNezet:geneticmap

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@LouisLeNezet

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This PR improve the genetic map convertion and normalisation module.
It now remove duplicated genetic distance and null rates values.

Some map file does contains null rate or repetition of genetic distance.
Most imputation tools crash with this kind of data resulting in unexpected, criptic behavior:

Segmentation fault in GLIMPSE2_PHASE, Error in if (sum(how_many_cols_below_0) > 0) { : value where TRUE/FALSE needed in STITCH for the single line at position 79150745 on chr9:

pos			rate		cm
79150210	0.44672897	80.085271
79150745	0			80.08551
79150746	0.44864865	80.08551
  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@LouisLeNezet LouisLeNezet self-assigned this Aug 31, 2026
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