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tasks/samtools.wdl
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| @@ -16,7 +16,7 @@ task samtools { | |||
| set -e | |||
| nt=$(nproc) | |||
| /opt/conda/bin/samtools view -@ $nt -bS ${sam} > ${bam} | |||
| /opt/conda/bin/samtools sort -@ $nt -m 2G ${bam} -o ${sorted_bam} | |||
| /opt/conda/bin/samtools sort -@ $nt -m 2GiB ${bam} -o ${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 -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${ins_size} | |||
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