.command.sh - Workdir - GERMLINE_CNV:CalcPanelCoverage (NA07891_c_01_gDNA_01_A23H3W5LT3_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/87/e7456aefa7f02f9aa516fbca474fa4/.command.sh
Size: 398 bytes
Task: GERMLINE_CNV:CalcPanelCoverage (NA07891_c_01_gDNA_01_A23H3W5LT3_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p NA07891_c_01_gDNA_01_A23H3W5LT3_1/
cnv_pipe calc-panel-coverage \
        NA07891_c_01_gDNA_01_A23H3W5LT3_1.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/NA07891_c_01_gDNA_01_A23H3W5LT3_1_counts.tsv \
        4 \
        20 \
        $(pwd)/NA07891_c_01_gDNA_01_A23H3W5LT3_1/