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cgroza / GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
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Fixes from bugs I encountered #27

Closed mikecuoco closed 6 months ago

mikecuoco commented 6 months ago
  1. Commit c04ccd9 - in bin/repmask_vcf.sh use samtools faidx + awk instead of awk alone to generate indels.length. awk alone was missing last seq in indels.fa
  2. Commit a6b622f - in main.nf merge_VCFs, use find instead of ls to generate vcf.list. If ls config includes colors, will break this step.
  3. Commit a7634fb - gzip the final GraffiTE merged genotypes to save storage
  4. Commit 9b92167 - add check if variant IDs are less than 50 characters, will produce error in RepeatMasker if not
cgroza commented 6 months ago

Hi!

Thank you for fixing these bugs. We merged the changes.

clemgoub commented 6 months ago

Thanks a lot @mikecuoco for your contribution! 🥳