Add HSMetrics

[marchoeppner]

Picard tools includes comprehensive metrics for exome analysis (target coverage, off target reads etc) - CollectHsMetrics.

Include this as a MultiQC input after duplicate marking

Example code (report attached): sample_custom_targets_only.html.zip

process runHybridCaptureMetrics {

    tag "${indivID}|${sampleID}"
    publishDir "${OUTDIR}/Common/${indivID}/${sampleID}/Processing/Picard_Metrics", mode: 'copy'

    input:
    set indivID, sampleID, file(bam), file(bai) from runPrintReadsOutput_for_HC_Metrics

    output:
    file(outfile) into HybridCaptureMetricsOutput mode flatten

    script:
    outfile = sampleID + ".hybrid_selection_metrics.txt"

    """
        java -XX:ParallelGCThreads=1 -Xmx${task.memory.toGiga()-mem_adjust}G -Djava.io.tmpdir=tmp/ -jar $PICARD CollectHsMetrics \
                INPUT=${bam} \
                OUTPUT=${outfile} \
                TARGET_INTERVALS=${TARGETS} \
                BAIT_INTERVALS=${BAITS} \
                REFERENCE_SEQUENCE=${REF} \
                TMP_DIR=tmp
        """
}