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Incorportate assembled mt genome #13

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Astahlke opened this issue Jul 16, 2021 · 1 comment

Collaborator

Astahlke commented Jul 16, 2021

Concat assembled MT contig Pgos/RawData/MT_Contig/Pgos_mtDNA_contig.fasta to primary assembly for polishing in arrow

The text was updated successfully, but these errors were encountered:

Contributor

j23414 commented Aug 16, 2021

Add a --mito_assembly (--mt_assembly?) or concat the mitocondrial genome before running.

if (params.mito_assembly){
  mito_ch = channel.of(params.mito_assembly, checkIfExists:true)
  asm_ch = channel.fromPath(params.primary_assembly, checkIfExists:true) | combine(mito_ch) | addMito
} else {
   asm_ch = channel.fromPath(params.primary_assembly, checkIfExists:true)
}

This is just a reminder to myself to add, after current run completes

j23414 closed this as completed

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