INNER CODE UNIT · Python

nsamp

franciscozorrilla/metaGEM · workflow/metaGEM.sh:196

nsamp=$(ls -d dataset/*/|wc -l)
echo "Raw data: $nsamp samples were identified in the dataset folder ... "

#qfilter: count .json report files
nqfilt=$(find qfiltered -name "*.json"|wc -l)
echo "Quality filtering: $nqfilt / $nsamp samples processed ... "
    
#assembly: count .gz fasta files
nassm=$(find assemblies -name "*.gz"|wc -l)
echo "Assembly: $nassm / $nsamp samples processed ... "
    
#concoct: count *concoct-bins subfolders
nconc=$(find concoct -name "*.concoct-bins"|wc -l)
echo "Binning (CONCOCT): $nconc / $nsamp samples processed ... "
    
#maxbin2: count *maxbin-bins subfolders
nmaxb=$(find maxbin -name "*.maxbin-bins"|wc -l)
echo "Binning (MaxBin2): $nmaxb / $nsamp samples processed ... "

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