瀏覽代碼

fix bug

master
YaqingLiu 5 年之前
父節點
當前提交
beb416c2d5
共有 1 個檔案被更改,包括 3 行新增1 行删除
  1. +3
    -1
      tasks/bcftools.wdl

+ 3
- 1
tasks/bcftools.wdl 查看文件

set -e set -e
mkdir -p /cromwell_root/tmp/bcftools mkdir -p /cromwell_root/tmp/bcftools


echo $vcf > b
for i in $vcf for i in $vcf
do do
bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz) bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz)


ls /cromwell_root/tmp/bcftools > a ls /cromwell_root/tmp/bcftools > a
cd /cromwell_root/tmp/bcftools cd /cromwell_root/tmp/bcftools
bcftools merge -m all -f PASS,. --force-samples *.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf
bcftools merge -m all -f PASS,. --force-samples *.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf
>>> >>>


runtime { runtime {
output { output {
File panel_of_normal_vcf = "panel_of_normal.vcf" File panel_of_normal_vcf = "panel_of_normal.vcf"
File a = "a" File a = "a"
File b = "b"
} }
} }

Loading…
取消
儲存