.command.sh - Workdir - GERMLINE_CNV:CalcPanelCoverage (NA12878_c_0003_gDNA_0002_A237FLHLT3_2)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/d68ebe7c2470c8150010b9edee8cd2/.command.sh
Size: 414 bytes
Task: GERMLINE_CNV:CalcPanelCoverage (NA12878_c_0003_gDNA_0002_A237FLHLT3_2)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p NA12878_c_0003_gDNA_0002_A237FLHLT3_2/
cnv_pipe calc-panel-coverage \
        NA12878_c_0003_gDNA_0002_A237FLHLT3_2.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/NA12878_c_0003_gDNA_0002_A237FLHLT3_2_counts.tsv \
        4 \
        20 \
        $(pwd)/NA12878_c_0003_gDNA_0002_A237FLHLT3_2/