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revise input

master
stead99 4 年前
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eaafbc8f29
共有 3 个文件被更改,包括 8 次插入1 次删除
  1. +2
    -0
      inputs
  2. +3
    -0
      tasks/fastqc.wdl
  3. +3
    -1
      workflow.wdl

+ 2
- 0
inputs 查看文件

{ "{{ project_name }}.read1": "{{ read1 }}", { "{{ project_name }}.read1": "{{ read1 }}",
"{{ project_name }}.read2": "{{ read2 }}", "{{ project_name }}.read2": "{{ read2 }}",
"{{ project_name }}.disk_size": "{{ disk_size }}",
"{{ project_name }}.cluster_config": "OnDemand bcs.a2.xlarge img-ubuntu-vpc",
"{{ project_name }}.fastqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5", "{{ project_name }}.fastqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
"{{ project_name }}.fastqscreen.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0", "{{ project_name }}.fastqscreen.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
"{{ project_name }}.screen_ref_dir": "/data/home/shangjun/JS_data/source_tree/source_tree/project_code/choppy_app/reference/fastq_screen_reference/", "{{ project_name }}.screen_ref_dir": "/data/home/shangjun/JS_data/source_tree/source_tree/project_code/choppy_app/reference/fastq_screen_reference/",

+ 3
- 0
tasks/fastqc.wdl 查看文件



runtime { runtime {
docker:docker docker:docker
systemDisk:"cloud_ssd 40"
cluster:cluster_config
dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
} }
output { output {
File read1_html = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.html") File read1_html = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.html")

+ 3
- 1
workflow.wdl 查看文件

call fastqc.fastqc as fastqc { call fastqc.fastqc as fastqc {
input: input:
read1=read1, read1=read1,
read2=read2
read2=read2,
docker=fastqc.docker
} }


call fastqscreen.fastq_screen as fastqscreen { call fastqscreen.fastq_screen as fastqscreen {
input: input:
read1=read1, read1=read1,
read2=read2, read2=read2,
docker=fastqscreen.docker,
screen_ref_dir=screen_ref_dir, screen_ref_dir=screen_ref_dir,
fastq_screen_conf=fastq_screen_conf fastq_screen_conf=fastq_screen_conf
} }

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