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comparison FLASH.sh @ 2:6889442b27dc draft default tip

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author aaronpetkau
date Sat, 04 Jul 2015 08:58:21 -0400
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1:a444685f161c 2:6889442b27dc
1 #/bin/bash
2
3 #grab output files
4 merged_reads=$1
5 shift
6 not_combined_1=$1
7 shift
8 not_combined_2=$1
9 shift
10 inter_not_combined=$1
11 shift
12 reads_and_pairs=$1
13 shift
14 log_file=$1
15 shift
16
17 flash $@ > $log_file
18 sleep 5 #sleep because phil says so
19
20 if [ -f out.notCombined_2.fastq ];
21 then
22 mv out.notCombined_2.fastq $not_combined_2
23 fi
24 if [ -f out.notCombined_1.fastq ];
25 then
26 mv out.notCombined_1.fastq $not_combined_1
27 fi
28 if [ -f out.notCombined.fastq ];
29 then
30 mv out.notCombined.fastq $inter_not_combined
31 fi
32 if [ -f out.readsAndPairs.tab ];
33 then
34 mv out.readsAndPairs.tab $reads_and_pairs
35 fi
36 if [ -f out.extendedFrags.fastq ];
37 then
38 mv out.extendedFrags.fastq $merged_reads
39 fi
40
41 exit 0