Mercurial > repos > mingchen0919 > aurora_fastqc

view build-and-run-job-scripts.sh @ 3:85351cdd4f19 draft

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planemo upload commit 61448862dc9016969191967aeefb7f7acce1e1f9
author mingchen0919
date Mon, 30 Apr 2018 16:40:21 -0400
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# run SHELL_SCRIPT within tool outputs directory
cd ${REPORT_FILES_PATH}

# build job-script.sh
cat >temp.sh <<EOF

cp ${X_r} read_1.fq
cp ${X_R} read_2.fq

fastqc \\
  -q \\
  -c ${X_c} \\
  -l ${X_l} \\
  ${X_d}/read_1.fq > /dev/null 2>&1
  
fastqc \\
  -q \\
  -c ${X_c} \\
  -l ${X_l} \\
  ${X_d}/read_2.fq > /dev/null 2>&1

EOF

grep -v None temp.sh > job-1-script.sh
rm temp.sh

# run SHELL_SCRIPT
sh job-1-script.sh


# unzip outputs
unzip -q read_1_fastqc.zip
unzip -q read_2_fastqc.zip