.command.sh - Workdir - DAQ:GERMLINE_CNV:CalcPanelCoverage (Sig_18_Blood)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/d0188555368c1b2134ec9c05435455/.command.sh
Size: 314 bytes
Task: DAQ:GERMLINE_CNV:CalcPanelCoverage (Sig_18_Blood)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p Sig_18_Blood/
cnv_pipe calc-panel-coverage \
        Sig_18_Blood.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/Sig_18_Blood_counts.tsv \
        4 \
        20 \
        $(pwd)/Sig_18_Blood/