1 ha cambiato i file con 2 aggiunte e 2 eliminazioni
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- 2
tasks/qualimapBAMqc.wdl
Vedi File
| set -e | set -e | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| awk 'BEGIN{OFS="\t"}{sub("\r","",$3);print $1,$2,$3,"",0,"."}' ${regions} > new.bed | awk 'BEGIN{OFS="\t"}{sub("\r","",$3);print $1,$2,$3,"",0,"."}' ${regions} > new.bed | ||||
| /opt/qualimap/qualimap bamqc -bam ${bam} -gff new.bed -outformat PDF:HTML -nt $nt -outdir ${bamname} --java-mem-size=32G | |||||
| tar -zcvf ${bamname}_qualimap.zip ${bamname} | |||||
| /opt/qualimap/qualimap bamqc -bam ${bam} -gff new.bed -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G | |||||
| tar -zcvf ${bamname}_bamqc_qualimap.zip ${bamname}_bamqc | |||||
| >>> | >>> | ||||
| runtime { | runtime { |
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