File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/8d35f2b15b1928f0e620f9cbab5ae1/.command.sh
Size
1018 bytes
Task
DAQ:BAM_POSTDEDUP_QC:SENTIEON_MULTIPLE_METRICS (1136_4Z5-T1-TDNA-1_A23MHWWLT4_1)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
sentieon driver \
    -t 31 \
    -r Homo_sapiens_assembly38.fasta \
    -i 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.bam \
     \
    --algo AlignmentStat 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.sentieon.alignment_summary_metrics \
    --algo InsertSizeMetricAlgo 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_metrics \
    --algo QualDistribution 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_distribution_metrics \
    --algo BaseDistributionByCycle 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.sentieon.base_distribution_by_cycle_metrics \
    --algo MeanQualityByCycle 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_by_cycle_metrics

sentieon plot InsertSizeMetricAlgo \
    -o 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_histogram.pdf \
    1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_metrics

cat <<-END_VERSIONS > versions.yml
"DAQ:BAM_POSTDEDUP_QC:SENTIEON_MULTIPLE_METRICS":
    sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS