1個のファイルの変更、1行の追加、1行の削除
+ 1
- 1
tasks/samtools.wdl
ファイルの表示
| set -e | set -e | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| /opt/conda/bin/samtools view -@ $nt -bS ${sam} > ${bam} | /opt/conda/bin/samtools view -@ $nt -bS ${sam} > ${bam} | ||||
| /opt/conda/bin/samtools sort -@ $nt -m 2GiB ${bam} -o ${sorted_bam} | |||||
| /opt/conda/bin/samtools sort -@ $nt -m 1000000000 ${bam} -o ${sorted_bam} | |||||
| /opt/conda/bin/samtools index -@ $nt ${sorted_bam} | /opt/conda/bin/samtools index -@ $nt ${sorted_bam} | ||||
| /opt/conda/bin/samtools stats -@ $nt ${sorted_bam} > ${samstats} | /opt/conda/bin/samtools stats -@ $nt ${sorted_bam} > ${samstats} | ||||
| /opt/conda/bin/samtools stats -@ $nt -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${ins_size} | /opt/conda/bin/samtools stats -@ $nt -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${ins_size} |
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