Create realignTargetCreator.cwl

[FarahZKhan]

To use it as stand alone tool - example: "cwltool realignerTargerCreator.cwl realignerTargerCreator.json". Still testing to make it work as a part of the workflow

[portah]

Repeatable arguments should not be hard copied also - it is good to use array

 - id: "#dbSNP"
    type: string
    default: "dbsnp_138.vcf"
    description: list of known variant files in vcf format
    inputBinding:
      position: 6
      prefix: "--known"

  - id: "#indelsMills"
    type: string
    default: "../data//GATK-complete-workflow/Ref_datasets/Mills_and_1000G_gold_st.vcf"
    description: list of known variant files in vcf format
    inputBinding:
      position: 7
      prefix: "--known"

  - id: "#indels1000G"
    type: string
    default: "../data//GATK-complete-workflow/Ref_datasets/1000G_phase1.indels.hg19.vcf"
    description: list of known variant files in vcf format
    inputBinding:
      position: 8
      prefix: "--known"

  - id: "#outputfile_realignTarget"
    type: string
    description: name of the output file from realignTargetCreator
    inputBinding:
      position: 9
      prefix: "-o"

outputs:
  - id: "#realignTargetCreator_output"
    type: "File"
    outputBinding: { glob: "realignTargetCreator_output.intervals" }

Hard copied output file name

[FarahZKhan]

@portah Done with the changes.

[portah]

There is an error in the file and job file please check

[FarahZKhan]

@portah I guess now the tool file and the job file is fixed now. Please check

[FarahZKhan]

reference.fai file and input.bam.bai file are required by GATK to process any bam file.

[portah]

I still confused by inputBinding: { position: 6, prefix: "--known" } you already have one

[FarahZKhan]

@portah yes that should just be position.