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GCNV ploidy_priors has hard coded contig names #489

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Nicolai-vKuegelgen opened this issue Feb 16, 2024 · 1 comment · Fixed by #490
Closed

GCNV ploidy_priors has hard coded contig names #489

Nicolai-vKuegelgen opened this issue Feb 16, 2024 · 1 comment · Fixed by #490

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@Nicolai-vKuegelgen
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Describe the bug
The GCNV model building requires prior values for contigs (=chromosome), which are hard coded into the corresponding snappy wrapper. However, the names of the contigs can be different depending of the soruce and version of the chromosome build on is using (i.e. GRCh37 vs GRCH38).

To Reproduce
Steps to reproduce the behavior:

  1. Use any genome reference that uses "chrN" styles (i.e. UCSC or most GRCh38 versions)
  2. Run any helper_gcnv_model step

Expected behavior
The file with ploidy_priors that snappy creates needs to have contig names matching the used reference files.

Additional context
This is the file which hardcodes the priors and currently contig names
https://github.com/bihealth/snappy-pipeline/blob/main/snappy_wrappers/wrappers/gcnv/contig_ploidy/wrapper.py

@Nicolai-vKuegelgen
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The previous fix introduced a new bug, because the {} brackets in the regex are first pasred by python/snakemake string formatting

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