diff --git a/pipeline.wdl b/pipeline.wdl index 9b4f299..56e9876 100644 --- a/pipeline.wdl +++ b/pipeline.wdl @@ -25,18 +25,13 @@ workflow pipeline { String project String cancer - String bed="/home/zhangchao/project/pipeline/workflow/script/public/bed/${probe}.bed" + String bed="$WORKFLOW/${probe}.bed" String ref = "/home/install/ref/hg19/hg19.fa" String workdir="${output_dir}" Map[String, Boolean] catecode - # call mytask.create_dir as create_dir { - # input: - # workdir=workdir - # } - call qc.qc as qc { input: run=catecode['addQc'], diff --git a/soft_bash b/soft_bash index 947580f..dbee65f 100755 --- a/soft_bash +++ b/soft_bash @@ -1,13 +1,13 @@ # 目录环境 export WORKFLOW=$(dirname "$(readlink -f "${BASH_SOURCE[0]}")") -export PUBLIC=$WORKFLOW/script/public +export PUBLIC=$WORKFLOW/codes/public export DATABASE=$WORKFLOW/database -# python -export PATH=/home/install/product/workflow/software/Python-3.8.11/bin:$PATH - # script export PATH=$WORKFLOW/codes:$PATH # software export PATH=$WORKFLOW/software/bin:$PATH + +# python +export PATH=/home/install/product/workflow/software/Python-3.8.11/bin:$PATH