INNER CODE UNIT · Python
nmwref
franciscozorrilla/metaGEM · workflow/metaGEM.sh:220
nmwref=$(ls -d refined_bins/*|wc -l)
echo "Bin refinement: $nmwref / $nsamp samples processed ... "
#metawrap_reassemble: count subfolders, also determine total number of final MAGs across samples
nmwrea=$(ls -d reassembled_bins/*|wc -l)
echo "Bin reassembly: $nmwrea / $nsamp samples processed ... "
#taxonomy: count subfolders
ntax=$(ls -d GTDBTk/*|wc -l)
echo "Taxonomy: $ntax / $nsamp samples processed ... "
#abundances: count subfolders
nabund=$(ls -d abundance/*|wc -l)
echo "Abundance: $nabund / $nsamp samples processed ... "
#models: count subfolders for sample progress and count .xml GEM files for total models generated
ngems=$(find GEMs -name "*xml"|wc -l)
ngemsamp=$(ls -d GEMs/*|wc -l)