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更新 'workflow.wdl'

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chenqingwang 4 years ago
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860e88a7ff
1 changed files with 19 additions and 15 deletions
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    -15
      workflow.wdl

+ 19
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workflow.wdl View File

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


workflow {{ project_name }} {
File reference
File bedfile
File bamfile
String sample_id String sample_id
File fa
File fai
File bed
File bam
File bai
String docker String docker
String cluster_config String cluster_config
String disk_size String disk_size


call BAMReadCount.BAMReadCount as BAMReadCount {
input:
reference = reference,
bedfile = bedfile,
bamfile = bamfile,
docker = docker,
disk_size = disk_size,
cluster_config=cluster_config,
sample_id=sample_id
command <<<
bam-readcount -f ${reference} -l ${bedfile} ${bamfile} > ${sample_id}.readcount
>>>

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

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

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