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revise workflow

master
stead99 4 years ago
parent
commit
6f3c5d9e27
2 changed files with 6 additions and 6 deletions
  1. +2
    -2
      inputs
  2. +4
    -4
      workflow.wdl

+ 2
- 2
inputs View File

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

+ 4
- 4
workflow.wdl View File

File fastq_screen_conf File fastq_screen_conf
File read1 File read1
File read2 File read2
String fastqc.docker
String fastqscreen.docker
String fastqc_docker
String fastqscreen_docker
String cluster_config String cluster_config


call fastqc.fastqc as fastqc { call fastqc.fastqc as fastqc {
read1=read1, read1=read1,
read2=read2, read2=read2,
cluster=cluster_config, cluster=cluster_config,
docker=fastqc.docker
docker=fastqc_docker
} }


call fastqscreen.fastq_screen as fastqscreen { call fastqscreen.fastq_screen as fastqscreen {
read1=read1, read1=read1,
read2=read2, read2=read2,
cluster=cluster_config, cluster=cluster_config,
docker=fastqscreen.docker,
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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