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1 parent 4ae1d0a commit c65e62dCopy full SHA for c65e62d
SneakerNet.plugins/assembleAll.pl
@@ -190,7 +190,9 @@ sub assembleAll{
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if(!-e "$outdir/quast/report.html"){
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logmsg "Running quast on $outassembly > $outdir/quast";
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- command("quast $outassembly --glimmer --output-dir $outdir/quast --threads $$settings{numcpus} --rna-finding");
+ # 2024-09-23 adding --min-contig 1 to accept assemblies of very small contig lengths:
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+ # we just want to know if it's a bad assembly and we don't want quast to crash.
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+ command("quast $outassembly --glimmer --output-dir $outdir/quast --threads $$settings{numcpus} --rna-finding --min-contig 1");
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}
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else{
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logmsg "Found $outdir/quast/report.html. Not rerunning";
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