.command.sh - Workdir - GERMLINE_CNV:CalcPanelCoverage (NA18523_c_0001_gDNA_0001_B23H2H2LT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/f4ecfd2fff791a51b1fa226751273b/.command.sh
Size: 414 bytes
Task: GERMLINE_CNV:CalcPanelCoverage (NA18523_c_0001_gDNA_0001_B23H2H2LT4_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p NA18523_c_0001_gDNA_0001_B23H2H2LT4_1/
cnv_pipe calc-panel-coverage \
        NA18523_c_0001_gDNA_0001_B23H2H2LT4_1.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/NA18523_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv \
        4 \
        20 \
        $(pwd)/NA18523_c_0001_gDNA_0001_B23H2H2LT4_1/