{
    "GATKJar": {
        "class": "File",
        "path": "/home/ubuntu/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar"
    },
    "inputBam_BaseRecalibrator": {
        "class": "File",
        "path": "/home/ubuntu/bespin-cwl/data/with-read-groups.bam"
    },
    "knownSites": [
        {
            "class": "File",
            "path": "/home/ubuntu/data/b37/dbsnp_138.b37.vcf.gz"
        },
        {
            "class": "File",
            "path": "/home/ubuntu/data/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz"
        }
    ],
    "bqsr": {
        "class": "File",
        "path": "/home/ubuntu/bespin-cwl/data/recal_data.table"
    },
    "out": "post_recal_data.table",
    "intervals": ["20"],
    "reference": {
        "class": "File",
        "path": "/home/ubuntu/data/b37/human_g1k_v37.fasta"
    }
}

{
    "GATKJar": {
        "class": "File",
        "path": "/home/ubuntu/GenomeAnalysisTK-3.7/GenomeAnalysisTK.jar"
    },
    "inputBam_BaseRecalibrator": {
        "class": "File",
        "path": "/home/ubuntu/bespin-cwl/data/with-read-groups.bam"
    },
    "knownSites": [
        {
            "class": "File",
            "path": "/home/ubuntu/data/b37/dbsnp_138.b37.vcf"
        },
        {
            "class": "File",
            "path": "/home/ubuntu/data/b37/Mills_and_1000G_gold_standard.indels.b37.vcf"
        }
    ],
    "bqsr": {
        "class": "File",
        "path": "/home/ubuntu/bespin-cwl/data/recal_data.table"
    },
    "outputfile_BaseRecalibrator": "post_recal_data.table",
    "intervals": ["20"],
    "reference": {
        "class": "File",
        "path": "/home/ubuntu/data/b37/human_g1k_v37.fasta"
    }
}

Update baserecalibrate-02 json for uncompressed vcf and corrected output file name
Update baserecalibrate-02 json for uncompressed vcf and corrected output file name

Next need to write CWL for baserecalibrate-03
