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jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis
GNU General Public License v3.0
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Argument checking in SqueezeMeta.pl would prevent the use of custom assemblers? #624

Closed fpusan closed 1 year ago

fpusan commented 1 year ago

This line in particular

if($assembler!~/megahit|spades|rnaspades|canu|flye/i) { $dietext.="UNRECOGNIZED assembler $assembler (valid ones are megahit, spades, canu or flye)\n"; }

would make the IDBA example in our PDF manual fail, I think. The list of valid assembler names should rather be gathered from the hash keys in %assemblers in SqueezeMeta_conf.pl.

jtamames commented 1 year ago

Hello @fpusan Thank you for your interest in SqueezeMeta! Yep, correct, that line should be corrected Best, J