|
7
|
1 # SHELL_SCRIPT file name
|
|
|
2 SHELL_SCRIPT='fastqc.sh'
|
|
|
3
|
|
|
4 # run SHELL_SCRIPT within tool outputs directory
|
|
|
5 cd ${REPORT_FILES_PATH}
|
|
|
6
|
|
|
7 # build job-script.sh
|
|
|
8 cat >temp.sh <<EOF
|
|
|
9
|
|
|
10 cp ${X_r} read_1.fq
|
|
|
11 cp ${X_R} read_2.fq
|
|
|
12
|
|
|
13 fastqc \\
|
|
|
14 -q \\
|
|
|
15 -c ${X_c} \\
|
|
|
16 -l ${X_l} \\
|
|
|
17 ${X_d}/read_1.fq > /dev/null 2>&1
|
|
|
18
|
|
|
19 fastqc \\
|
|
|
20 -q \\
|
|
|
21 -c ${X_c} \\
|
|
|
22 -l ${X_l} \\
|
|
|
23 ${X_d}/read_2.fq > /dev/null 2>&1
|
|
|
24
|
|
|
25 EOF
|
|
|
26
|
|
|
27 grep -v None temp.sh > ${SHELL_SCRIPT}
|
|
|
28 rm temp.sh
|
|
|
29
|
|
|
30 # run SHELL_SCRIPT
|
|
|
31 sh ${SHELL_SCRIPT}
|
|
|
32
|
|
|
33
|
|
|
34 # unzip outputs
|
|
|
35 unzip -q read_1_fastqc.zip
|
|
|
36 unzip -q read_2_fastqc.zip |
