.command.sh - Workdir - DAQ:GERMLINE_CNV:CalcPanelCoverage (1029_01S-N1-BDNA-1_B23KGCJLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/e50f27f37cb3df75d50ba6c74771e3/.command.sh
Size: 390 bytes
Task: DAQ:GERMLINE_CNV:CalcPanelCoverage (1029_01S-N1-BDNA-1_B23KGCJLT4_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p 1029_01S-N1-BDNA-1_B23KGCJLT4_1/
cnv_pipe calc-panel-coverage \
        1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/1029_01S-N1-BDNA-1_B23KGCJLT4_1_counts.tsv \
        4 \
        20 \
        $(pwd)/1029_01S-N1-BDNA-1_B23KGCJLT4_1/