#!/bin/bash

# This wrapper is for SPAdes 3.15.5 on Expanse.

export MODULEPATH=/expanse/projects/ngbt/opt/expanse/modules:$MODULEPATH
module load spades/3.15.5


start=$(date +%s)
spades.py $*
/expanse/projects/ngbt/opt/expanse/N50-fasta.pl */contigs.fasta > contigs.N50
end=$(date +%s)
elapsed=$((end-start))
echo Elapsed time = $elapsed s

for f in *; do
    if [[ -d $f ]]; then
        jar cvf ${f}.zip $f
        echo "archived subdir $f as ${f}.zip"
    fi
done
echo "... moving on"