"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" | |||||
} | } |
"{{ 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 }}" |
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" | |||||
} | |||||
} | } |
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 | |||||
} | |||||
} | } |