Mercurial > repos > aaronpetkau > flash
diff FLASH.sh @ 2:6889442b27dc draft default tip
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| author | aaronpetkau |
|---|---|
| date | Sat, 04 Jul 2015 08:58:21 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FLASH.sh Sat Jul 04 08:58:21 2015 -0400 @@ -0,0 +1,41 @@ +#/bin/bash + +#grab output files +merged_reads=$1 +shift +not_combined_1=$1 +shift +not_combined_2=$1 +shift +inter_not_combined=$1 +shift +reads_and_pairs=$1 +shift +log_file=$1 +shift + +flash $@ > $log_file +sleep 5 #sleep because phil says so + +if [ -f out.notCombined_2.fastq ]; +then + mv out.notCombined_2.fastq $not_combined_2 +fi +if [ -f out.notCombined_1.fastq ]; +then + mv out.notCombined_1.fastq $not_combined_1 +fi +if [ -f out.notCombined.fastq ]; +then + mv out.notCombined.fastq $inter_not_combined +fi +if [ -f out.readsAndPairs.tab ]; +then + mv out.readsAndPairs.tab $reads_and_pairs +fi +if [ -f out.extendedFrags.fastq ]; +then + mv out.extendedFrags.fastq $merged_reads +fi + +exit 0