.command.sh - Workdir - GERMLINE_CNV:CalcPanelCoverage (1173_NFO-N2-BDNA-01_B23L5TMLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/3e439fb77cbc719ba96aaebc80ffe1/.command.sh
Size: 394 bytes
Task: GERMLINE_CNV:CalcPanelCoverage (1173_NFO-N2-BDNA-01_B23L5TMLT4_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p 1173_NFO-N2-BDNA-01_B23L5TMLT4_1/
cnv_pipe calc-panel-coverage \
        1173_NFO-N2-BDNA-01_B23L5TMLT4_1.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/1173_NFO-N2-BDNA-01_B23L5TMLT4_1_counts.tsv \
        4 \
        20 \
        $(pwd)/1173_NFO-N2-BDNA-01_B23L5TMLT4_1/