2 changed files with 11 additions and 3 deletions
tasks/align.wdl → tasks/mixcr.wdl
View File
| task align { | |||||
| task mixcr { | |||||
| File read1 | File read1 | ||||
| File read2 | File read2 | ||||
| command <<< | command <<< | ||||
| mixcr align -p rna-seq -s hsa -OallowPartialAlignments=true ${read1} ${read2} ${base}.vdjca | mixcr align -p rna-seq -s hsa -OallowPartialAlignments=true ${read1} ${read2} ${base}.vdjca | ||||
| mixcr assemblePartial ${base}.vdjca ${base}_rescued_1.vdjca | |||||
| mixcr assemblePartial ${base}_rescued_1.vdjca ${base}_rescued_2.vdjca | |||||
| mixcr extend ${base}_rescued_2.vdjca ${base}_rescued_2_extended.vdjca | |||||
| mixcr assemble ${base}_rescued_2_extended.vdjca ${base}.clns | |||||
| mixcr exportClones ${base}.clns ${base}.txt | |||||
| mixcr exportClones -c TRB ${base}.clns ${base}.TRB.txt | |||||
| mixcr exportClones -c IGH ${base}.clns ${base}.IGH.txt | |||||
| >>> | >>> | ||||
| runtime { | runtime { |
+ 2
- 2
workflow.wdl
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| import "./tasks/align.wdl" as align | |||||
| import "./tasks/mixcr.wdl" as mixcr | |||||
| workflow {{ project_name }} { | workflow {{ project_name }} { | ||||
| String disk_size | String disk_size | ||||
| call align.align as align { | |||||
| call mixcr.mixcr as mixcr { | |||||
| input: | input: | ||||
| read1=read1, | read1=read1, | ||||
| read2=read2, | read2=read2, |
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