Replace blast by diamond

hoelzer / pocp

Calculation of the Percentage of Conserved Proteins following Qin, Xie et al. 2014 but using DIAMOND instead of BLASTP for alignments.

GNU General Public License v3.0

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Replace blast by diamond #10

Closed michoug closed 1 year ago

michoug commented 1 year ago

Hi @hoelzer, Just a small pull request to replace Blast with Diamond. Diamond is much faster than blast with similar sensitivity (https://www.nature.com/articles/s41592-021-01101-x) and I want to compare a lot of genomes so a speed bump is very much appreciated Best Greg

michoug commented 1 year ago

I'm not an expert on nextflow and I run the command with -profile local,mamba. I don't know if anything should be changed in regards to Docker or slurm

michoug commented 1 year ago

Sorry some bugs inside