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@@ -12,8 +12,8 @@ task qualimapBAMqc { |
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set -e |
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nt=$(nproc) |
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awk 'BEGIN{OFS="\t"}{sub("\r","",$3);print $1,$2,$3,"",0,"."}' ${regions} > new.bed |
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/opt/qualimap/qualimap bamqc -bam ${bam} -gff new.bed -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=32G |
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tar -zcvf ${bamname}_qualimap.zip ${bamname} |
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/opt/qualimap/qualimap bamqc -bam ${bam} -gff new.bed -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G |
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tar -zcvf ${bamname}_bamqc_qualimap.zip ${bamname}_bamqc |
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>>> |
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runtime { |