Closed FarahZKhan closed 8 years ago
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
@portah Done with the changes.
There is an error in the file and job file please check
@portah I guess now the tool file and the job file is fixed now. Please check
reference.fai file and input.bam.bai file are required by GATK to process any bam file.
I still confused by inputBinding: { position: 6, prefix: "--known" } you already have one
@portah yes that should just be position.
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