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pipeline
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bug

master
chaopower 2023-12-15 13:25:10 +08:00
parent 8bc3bf2668
commit 1df27e6079
2 changed files with 5 additions and 10 deletions
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7
pipeline.wdl
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@ -25,18 +25,13 @@ workflow pipeline {
String project String project
String cancer String cancer
String bed="/home/zhangchao/project/pipeline/workflow/script/public/bed/${probe}.bed" String bed="$WORKFLOW/${probe}.bed"
String ref = "/home/install/ref/hg19/hg19.fa" String ref = "/home/install/ref/hg19/hg19.fa"
String workdir="${output_dir}" String workdir="${output_dir}"
Map[String, Boolean] catecode Map[String, Boolean] catecode
# call mytask.create_dir as create_dir {
# input:
# workdir=workdir
# }
call qc.qc as qc { call qc.qc as qc {
input: input:
run=catecode['addQc'], run=catecode['addQc'],

8
soft_bash
View File

@ -1,13 +1,13 @@
# 目录环境 # 目录环境
export WORKFLOW=$(dirname "$(readlink -f "${BASH_SOURCE[0]}")") export WORKFLOW=$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")
export PUBLIC=$WORKFLOW/script/public export PUBLIC=$WORKFLOW/codes/public
export DATABASE=$WORKFLOW/database export DATABASE=$WORKFLOW/database
# python
export PATH=/home/install/product/workflow/software/Python-3.8.11/bin:$PATH
# script # script
export PATH=$WORKFLOW/codes:$PATH export PATH=$WORKFLOW/codes:$PATH
# software # software
export PATH=$WORKFLOW/software/bin:$PATH export PATH=$WORKFLOW/software/bin:$PATH
# python
export PATH=/home/install/product/workflow/software/Python-3.8.11/bin:$PATH