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Copy pathreal_data_count_extraction.xml
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real_data_count_extraction.xml
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<?xml version="1.0" encoding="UTF-8"?>
<watchdog xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="watchdog.xsd" watchdogBase="/home/proj/software/watchdog/">
<settings>
<constants>
<const name="WATCHDOG">/home/proj/software/watchdog</const>
<const name="BASE">/mnt/raidinput2/tmp/hadziahmetovic/DiffSplicing-workflow</const>
<const name="INPUT_TABLE">${BASE}/real_data.table</const>
<const name="LOGDIR">/mnt/raidinput2/tmp/hadziahmetovic/empires_2021/LOG/</const>
<const name="INDEXDIR">/mnt/raidinput2/tmp/hadziahmetovic/index/Homo_sapiens.GRCh38.103</const>
<const name="GTF">/mnt/raidinput2/tmp/hadziahmetovic/index/annotation/Homo_sapiens.GRCh38.103.gtf</const>
<const name="FASTA">/mnt/raidinput2/tmp/hadziahmetovic/index/annotation/Homo_sapiens.GRCh38.dna.primary_assembly.fa</const>
<const name="NTHREAD">32</const>
</constants>
<executors>
<sge name="star" maxRunning="5" slots="1" memory="105000M"/>
<sge name="emp" maxRunning="5" slots="1" memory="70000M"/>
</executors>
<processBlock>
<processTable name="table" table="${INPUT_TABLE}"/>
</processBlock>
</settings>
<tasks mail="hadziahmetovic@cip.ifi.lmu.de">
<scriptCallerTask id="1" name="hisat" executor="emp" processBlock="table">
<parameter>
<script>${BASE}/config/run_hisat.sh</script>
<param>index:${INDEXDIR}</param>
<param>pdata:{$pdata}</param>
<param>samples:{$samples}</param>
<param>out:{$out}</param>
<param>nthread:${NTHREAD}</param>
<param>log:${LOGDIR}</param>
</parameter>
<streams>
<stdout>${LOGDIR}/hisat2_{$dir}.out</stdout>
<stderr>${LOGDIR}/hisat2_{$dir}.err</stderr>
</streams>
</scriptCallerTask>
<scriptCallerTask id="2" name="star" executor="star" processBlock="table">
<parameter>
<script>${BASE}/config/run_star.sh</script>
<!--config>${BASE}/config/star.config</config-->
<param>index:${INDEXDIR}</param>
<param>pdata:{$pdata}</param>
<param>samples:{$samples}</param>
<param>out:{$out}</param>
<param>nthread:${NTHREAD}</param>
<param>log:${LOGDIR}</param>
</parameter>
<streams>
<stdout>${LOGDIR}/star_{$dir}.out</stdout>
<stderr>${LOGDIR}/star_{$dir}.err</stderr>
</streams>
</scriptCallerTask>
<scriptCallerTask id="3" name="featureCounts" executor="emp" processBlock="table">
<dependencies>
<depends separate="true">1</depends>
<depends separate="true">2</depends>
</dependencies>
<parameter>
<script>${BASE}/config/run_featureCounts.sh</script>
<param>index:${INDEXDIR}</param>
<param>gtf:${GTF}</param>
<param>pdata:{$pdata}</param>
<param>out:{$out}</param>
<param>nthread:${NTHREAD}</param>
<param>log:${LOGDIR}</param>
<param>hisat2</param>
<param>star</param>
</parameter>
<streams>
<stdout>${LOGDIR}/featureCounts_{$dir}.out</stdout>
<stderr>${LOGDIR}/featureCounts_{$dir}.err</stderr>
</streams>
</scriptCallerTask>
<scriptCallerTask id="4" name="eval" executor="emp" processBlock="table">
<dependencies>
<depends separate="true">3</depends>
</dependencies>
<parameter>
<script>${BASE}/config/eval_real_data.sh</script>
<param>gtf:${GTF}</param>
<param>pdata:{$pdata}</param>
<param>out:{$out}</param>
<param>nthread:${NTHREAD}</param>
<param>log:${LOGDIR}</param>
<param>hisat2</param>
<param>star</param>
<param>base:${BASE}/config</param>
</parameter>
<streams>
<stdout>${LOGDIR}/eval_{$dir}.out</stdout>
<stderr>${LOGDIR}/eval_{$dir}.err</stderr>
</streams>
</scriptCallerTask>
<!--scriptCallerTask id="3" name="trCount" executor="emp" processBlock="table">
<dependencies>
<depends separate="true">2</depends>
</dependencies>
<parameter>
<script>${BASE}/config/trcount.sh</script>
<param>gtf:${GTF}</param>
<param>out:{$out}</param>
<param>log:${LOGDIR}</param>
</parameter>
<streams>
<stdout>${LOGDIR}/trcount_{$dir}.out</stdout>
<stderr>${LOGDIR}/trcount_{$dir}.err</stderr>
</streams>
</scriptCallerTask-->
</tasks>
</watchdog>