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name of bam

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LUYAO REN 5 年之前
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eadb428a24
共有 1 個檔案被更改,包括 3 行新增3 行删除
  1. +3
    -3
      tasks/mapping.wdl

+ 3
- 3
tasks/mapping.wdl 查看文件

@@ -18,7 +18,7 @@ task mapping {
set -e
export SENTIEON_LICENSE=192.168.0.55:8990
nt=$(nproc)
${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}.${type}\tSM:${sample}.${type}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${sample}.sorted.bam -t $nt --sam2bam -i -
${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}.${type}\tSM:${sample}.${type}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${sample}.${type}.sorted.bam -t $nt --sam2bam -i -
>>>

runtime {
@@ -28,7 +28,7 @@ task mapping {
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}
output {
File sorted_bam = "${sample}.sorted.bam"
File sorted_bam_index = "${sample}.sorted.bam.bai"
File sorted_bam = "${sample}.${type}.sorted.bam"
File sorted_bam_index = "${sample}.${type}.sorted.bam.bai"
}
}

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