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|
#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: CommandLineTool
hints:
- class: ResourceRequirement
coresMin: 2
- class: DockerRequirement
dockerPull: docker.io/python:3-slim
inputs:
- id: reference
type: File
inputBinding: { position: 2 }
- id: reads
type:
type: array
items: File
inputBinding: { position: 3 }
- id: minimum_seed_length
type: int
inputBinding: { position: 1, prefix: -m }
- id: min_std_max_min
type: { type: array, items: int }
inputBinding:
position: 1
prefix: -I
itemSeparator: ","
- id: args.py
type: File
default:
class: File
location: args.py
inputBinding:
position: -1
outputs:
- id: sam
type: ["null", File]
outputBinding: { glob: output.sam }
- id: args
type:
type: array
items: string
baseCommand: python
arguments:
- bwa
- mem
- valueFrom: $(runtime.cores)
position: 1
prefix: -t
stdout: output.sam
|
