.command.sh - Workdir - CNV_PIPE:CalcPanelCoverage (FC13_cnv_mosaic_calc_panel_coverage_3700651334_r13)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/67/1ea854f05331fca0624d8d66618213/.command.sh
Size: 320 bytes
Task: CNV_PIPE:CalcPanelCoverage (FC13_cnv_mosaic_calc_panel_coverage_3700651334_r13)
Attempt

Content

#!/bin/bash -Ceuo pipefail
echo "$(pwd)"
mkdir  -p 3700651334_r13/
cnv_pipe calc-panel-coverage \
        3700651334_r13.bam \
        Renasight_CNV.mosatic.tm.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/counts.tsv \
        1 \
        20 \
        $(pwd)/3700651334_r13/ \