#!/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