view build-and-run-job-scripts.sh @ 6:afa1774dc49b draft default tip

planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 10:26:31 -0500
parents 803f4888f36a
children
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# run job scripts within the tool outputs directory
cd ${REPORT_FILES_PATH}

#========== build and run job 1 script ============
cat >htseq-count.sh <<EOF
 htseq-count \\
    $(echo ${X_A} | sed 's/,/ /g') \\
    ${X_G} \\
    -f ${X_f} \\
    -r ${X_r} \\
    -s ${X_S} \\
    -a ${X_a} \\
    -t ${X_T} \\
    -i ${X_i} \\
    -m ${X_m} > htseq-counts-raw.txt

  grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' htseq-counts-raw.txt > counts.txt

EOF

# run job 1 script
sh htseq-count.sh