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Aded BUSCO ideogram for GENOME mode #102

Merged
merged 5 commits into from
Dec 10, 2024
Merged

Aded BUSCO ideogram for GENOME mode #102

merged 5 commits into from
Dec 10, 2024

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FernandoDuarteF
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Close #98.

Changes

  1. Added plot_makers1.R and adapted genome_ideogram.nf from the BUSCO support protocol 2.
  2. Changed version of BUSCO in busco/busco/main.nf module to v5.8.0 (see BUSCO doesn't keep the original chromosomes IDs on test dataset #97).

Comments

Probably some code cleaning is necessary before merging, specially regarding the R scripts. Other than that, this is working as expected, at least on the test dataset.

@FernandoDuarteF FernandoDuarteF changed the title Aded ideogram for GENOME mode Aded BUSCO ideogram for GENOME mode Dec 6, 2024
@FernandoDuarteF FernandoDuarteF self-assigned this Dec 6, 2024
@FernandoDuarteF
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Perhaps it would be a good idea to have a single module for the BUSCO ideogram, as now there is one for genome only mode (renamed to genome_only_busco_ideogram.nf) and one for genome and annotation (renamed to genome_annotation_busco_ideogram.nf).

We shoould also rename some scripts in the /bin folder to make them more descriptive. I'll deal with this later.

@chriswyatt1
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We could just add this to another issue for now. Yes, would make sense to have in once module, but I think this way is fine for now

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Just a few little things to change, commented later

@FernandoDuarteF
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I thinks this is ready to merge.

@FernandoDuarteF FernandoDuarteF merged commit e7df634 into dev Dec 10, 2024
@FernandoDuarteF FernandoDuarteF deleted the genome_ideogram branch December 10, 2024 14:10
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BUSCO_IDEOGRAM for GENOME mode
2 participants