.command.sh - Workdir - GERMLINE_CNV:CalcPanelCoverage (NA01535_c_0001_gDNA_0001_A23H3W5LT3_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/13f08ea7ef89dd24948097549a7b55/.command.sh
Size: 414 bytes
Task: GERMLINE_CNV:CalcPanelCoverage (NA01535_c_0001_gDNA_0001_A23H3W5LT3_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p NA01535_c_0001_gDNA_0001_A23H3W5LT3_1/
cnv_pipe calc-panel-coverage \
        NA01535_c_0001_gDNA_0001_A23H3W5LT3_1.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/NA01535_c_0001_gDNA_0001_A23H3W5LT3_1_counts.tsv \
        4 \
        20 \
        $(pwd)/NA01535_c_0001_gDNA_0001_A23H3W5LT3_1/