57 lines
1.5 KiB
Plaintext
57 lines
1.5 KiB
Plaintext
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task runstatistics {
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String name
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String outputDir
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String rmdupBam
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String ref
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String codesDir
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String bed
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command <<<
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if [ ! -d ${outputDir}/qc/${name}_bamdst ];then
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mkdir -p ${outputDir}/qc/${name}_bamdst
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fi
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samtools flagstat -@ 10 ${rmdupBam} >${outputDir}/qc/${name}.rmdup.flagstat
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samtools stats --reference ${ref} -t ${bed} -@ 10 ${rmdupBam} > ${outputDir}/qc/${name}.rmdup.stat
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bamdst -p ${bed} -o ${outputDir}/qc/${name}_bamdst ${rmdupBam}
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Rscript ${codesDir}/InsertAndDepthStat.R \
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${outputDir}/qc/${name}_InsertAndDepthStat \
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${outputDir}/qc/${name}_bamdst/insertsize.plot \
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${outputDir}/qc/${name}_bamdst/depth_distribution.plot
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>>>
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}
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workflow statistics {
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String tumor
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String tumor_rmdupBam
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String? normal
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String? normal_rmdupBam
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String ref
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String bed
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String outputDir
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String codesDir
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scatter(name in [tumor, normal]) {
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if (defined(name)) {
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call runstatistics {
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input:
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name=name,
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outputDir=outputDir,
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rmdupBam=if name==tumor then tumor_rmdupBam else normal_rmdupBam,
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ref=ref,
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codesDir=codesDir,
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bed=bed
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}
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}
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}
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output {
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String tumor_bamdst_depth = "${outputDir}/qc/${tumor}_bamdst/depth.tsv.gz"
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}
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}
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