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view build-and-run-job-scripts.sh @ 2:c64267b9f754 draft default tip

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planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 12:48:14 -0500
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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 > read_1.log.txt 2>&1
  
fastqc \\
  -q \\
  -c ${X_c} \\
  -l ${X_l} \\
  ${X_d}/read_2.fq > read_2.log.txt 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