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Update: sample_id in Haplotyper and Pindel

master
YaqingLiu 3 年之前
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f4c1c1aba5
共有 1 個文件被更改,包括 4 次插入4 次删除
  1. +4
    -4
      workflow.wdl

+ 4
- 4
workflow.wdl 查看文件

input: input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR, SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
SENTIEON_LICENSE=SENTIEON_LICENSE, SENTIEON_LICENSE=SENTIEON_LICENSE,
sample=sample_id,
sample=sample_id + '.N',
fasta=fasta, fasta=fasta,
ref_dir=ref_dir, ref_dir=ref_dir,
recaled_bam=normal_BQSR.recaled_bam, recaled_bam=normal_BQSR.recaled_bam,
if (pindel) { if (pindel) {
call Pindel.Pindel as Pindel { call Pindel.Pindel as Pindel {
input: input:
sample_id=sample_id,
sample_id=sample_id + '.N',
bam=normal_BQSR.recaled_bam, bam=normal_BQSR.recaled_bam,
bam_index=normal_BQSR.recaled_bam_index, bam_index=normal_BQSR.recaled_bam_index,
fasta=fasta, fasta=fasta,
input: input:
SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR, SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
SENTIEON_LICENSE=SENTIEON_LICENSE, SENTIEON_LICENSE=SENTIEON_LICENSE,
sample=sample_id,
sample=sample_id + '.N',
fasta=fasta, fasta=fasta,
ref_dir=ref_dir, ref_dir=ref_dir,
recaled_bam=normal_BQSR_fb.recaled_bam, recaled_bam=normal_BQSR_fb.recaled_bam,
if (pindel) { if (pindel) {
call Pindel.Pindel as Pindel_fb { call Pindel.Pindel as Pindel_fb {
input: input:
sample_id=sample_id,
sample_id=sample_id + '.N',
bam=normal_BQSR_fb.recaled_bam, bam=normal_BQSR_fb.recaled_bam,
bam_index=normal_BQSR_fb.recaled_bam_index, bam_index=normal_BQSR_fb.recaled_bam_index,
fasta=fasta, fasta=fasta,

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