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master
YaqingLiu 4 years ago
parent
commit
62f2616cc5
4 changed files with 56 additions and 49 deletions
  1. +4
    -2
      defaults
  2. +2
    -1
      inputs
  3. +23
    -22
      tasks/BAMReadCount.wdl
  4. +27
    -24
      workflow.wdl

+ 4
- 2
defaults View File

"fa": "GRCh38.d1.vd1.fa", "fa": "GRCh38.d1.vd1.fa",
"ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/", "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
"disk_size": "200", "disk_size": "200",
"docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bamreadcount:v0.8.0",
"cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc"
"docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bamreadcount:v0.8.0",
"cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
"min_base_quality": "0",
"min_mapping_quality": "0"
} }

+ 2
- 1
inputs View File

"{{ project_name }}.docker": "{{ docker }}", "{{ project_name }}.docker": "{{ docker }}",
"{{ project_name }}.ref_dir": "{{ ref_dir }}", "{{ project_name }}.ref_dir": "{{ ref_dir }}",
"{{ project_name }}.fa": "{{ fa }}", "{{ project_name }}.fa": "{{ fa }}",
"{{ project_name }}.fai": "{{ fai }}",
"{{ project_name }}.bed": "{{ bed }}", "{{ project_name }}.bed": "{{ bed }}",
"{{ project_name }}.bam": "{{ bam }}", "{{ project_name }}.bam": "{{ bam }}",
"{{ project_name }}.bai": "{{ bai }}", "{{ project_name }}.bai": "{{ bai }}",
"{{ project_name }}.min_mapping_quality": "{{ min_mapping_quality }}",
"{{ project_name }}.min_base_quality": "{{ min_base_quality }}",
"{{ project_name }}.disk_size": "{{ disk_size }}", "{{ project_name }}.disk_size": "{{ disk_size }}",
"{{ project_name }}.cluster_config": "{{ cluster_config }}", "{{ project_name }}.cluster_config": "{{ cluster_config }}",
"{{ project_name }}.sample_id": "{{ sample_id }}" "{{ project_name }}.sample_id": "{{ sample_id }}"

+ 23
- 22
tasks/BAMReadCount.wdl View File

task BAMReadCount { task BAMReadCount {


String sample_id
File ref_dir
String fa
File fai
File bed
File bam
File bai
String docker
String cluster_config
String disk_size
String sample_id
File ref_dir
String fa
File bed
File bam
File bai
String min_mapping_quality
String min_base_quality
String docker
String cluster_config
String disk_size


command <<<
bam-readcount -w 0 -q1 -f ${ref_dir}/${fa} -l ${bed} ${bam} > ${sample_id}.readcount
>>>
command <<<
bam-readcount -w 0 -q ${min_mapping_quality} -b ${min_base_quality} -f ${ref_dir}/${fa} -l ${bed} ${bam} > ${sample_id}.readcount
>>>


runtime {
docker: docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}
runtime {
docker: docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}


output {
File BAMReadCount = "${sample_id}.readcount"
}
output {
File BAMReadCount = "${sample_id}.readcount"
}
} }

+ 27
- 24
workflow.wdl View File

import "./tasks/BAMReadCount.wdl" as BAMReadCount import "./tasks/BAMReadCount.wdl" as BAMReadCount


workflow {{ project_name }} { workflow {{ project_name }} {
File ref_dir
String fa
File fai
File bed
File bam
File bai
String sample_id
String docker
String cluster_config
String disk_size
File ref_dir
String fa
File bed
File bam
File bai
String min_mapping_quality
String min_base_quality
String sample_id
String docker
String cluster_config
String disk_size


call BAMReadCount.BAMReadCount as BAMReadCount {
input:
ref_dir=ref_dir,
fa=fa,
fai=fai,
bed=bed,
bam=bam,
bai=bai,
docker=docker,
disk_size=disk_size,
cluster_config=cluster_config,
sample_id=sample_id
}
call BAMReadCount.BAMReadCount as BAMReadCount {
input:
ref_dir=ref_dir,
fa=fa,
fai=fai,
bed=bed,
bam=bam,
bai=bai,
min_mapping_quality=min_mapping_quality,
min_base_quality=min_base_quality,
docker=docker,
disk_size=disk_size,
cluster_config=cluster_config,
sample_id=sample_id
}
} }

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