linzipeng
6 years ago
1 changed files with 4 additions and 4 deletions
+ 4
- 4
workflow.wdl
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| import "./tasks/Trim.wdl" as Trim | import "./tasks/Trim.wdl" as Trim | ||||
| import "./tasks/Mapping.wdl" as Meapping | |||||
| import "./tasks/Mapping.wdl" as Mapping | |||||
| import "./tasks/Dedup.wdl" as Dedup | import "./tasks/Dedup.wdl" as Dedup | ||||
| import "./tasks/Call_meth.wdl" as Call_meth | import "./tasks/Call_meth.wdl" as Call_meth | ||||
| call BQSR.BQSR as BQSR { | |||||
| call Trim.Trim as Trim { | |||||
| input: | input: | ||||
| sample=sample, | sample=sample, | ||||
| ref_dir=ref_dir, | ref_dir=ref_dir, | ||||
| disk_size=disk_size, | disk_size=disk_size, | ||||
| cluster_config=cluster_config | cluster_config=cluster_config | ||||
| } | } | ||||
| call mapping.mapping as mapping { | |||||
| call Mapping.Mapping as Mapping { | |||||
| input: | input: | ||||
| sample=sample, | sample=sample, | ||||
| ref_dir=ref_dir, | ref_dir=ref_dir, | ||||
| disk_size=disk_size, | disk_size=disk_size, | ||||
| cluster_config=cluster_config | cluster_config=cluster_config | ||||
| } | } | ||||
| call Haplotyper.Haplotyper as Haplotyper { | |||||
| call Call_meth.Call_meth as Call_meth { | |||||
| input: | input: | ||||
| ref_dir=ref_dir, | ref_dir=ref_dir, | ||||
| Dedup_bam=Dedup_R1_val_1_bismark_bt2_pe.deduplicated.bam, | Dedup_bam=Dedup_R1_val_1_bismark_bt2_pe.deduplicated.bam, |
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