Tranches optimization

[abhi18av]

• Integrate the minVQSLod value from the tranches file in the optimization subworkflow
• Test the optimization workflow (dataset)
• Accommodate the publication of BAM files via GATK_HAPLOTYPE_CALLER_*
• Add the Graphviz DOT file

[abhi18av]

With the addition of this PR, there would be a new file published (for logging purposes) in /cohort/snp_variant_files/vqsr/best_annotations/all_annotations_data.json enumerating the annotation order and minVQSLod values or these annotations.

📗 The best annotation below was determined to be ANN3 with minVQSLod value to be -414.2304

[
    {
        "minVQSLod": "-8418.0842",
        "annotationsOrder": " DP, AS_MQ, AS_QD, AS_FS, AS_MQRankSum, AS_SOR, AS_ReadPosRankSum",
        "annotationsCount": "ANN7"
    },
    {
        "minVQSLod": "-8444.1324",
        "annotationsOrder": " DP, AS_MQ, AS_QD, AS_FS, AS_MQRankSum, AS_SOR",
        "annotationsCount": "ANN6"
    },
    {
        "minVQSLod": "-8467.8560",
        "annotationsOrder": " DP, AS_MQ, AS_QD, AS_FS, AS_MQRankSum",
        "annotationsCount": "ANN5"
    },
    {
        "minVQSLod": "-414.3786",
        "annotationsOrder": " DP, AS_MQ, AS_QD, AS_FS",
        "annotationsCount": "ANN4"
    },
    {
        "minVQSLod": "-414.2304",
        "annotationsOrder": " DP, AS_MQ, AS_QD",
        "annotationsCount": "ANN3"
    },
    {
        "minVQSLod": "-415.0220",
        "annotationsOrder": " DP, AS_MQ",
        "annotationsCount": "ANN2"
    }
]

[abhi18av]

@TimHHH and @LennertVerboven , could you please take this branch tranches-optimization for a spin on your cluster and datasets?

If all looks good then please go ahead and merge this.

[TimHHH]

@abhi18av what is this 'Graphviz DOT file' and what is its purpose?

[abhi18av]

@TimHHH that file is basically the graph which gets generated, we can use that to create a PNG of the flow. It doesn't change anything in the pipeline.

Apart from that, is this branch working as expected?

[TimHHH]

all good, nice