.command.sh - Workdir - GERMLINE_CNV:CalcPanelCoverage (NA17264_c_01_gDNA_01_B23H3TCLT3_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/76df8d3575c6fa3f1ae3bc0bb430ca/.command.sh
Size: 398 bytes
Task: GERMLINE_CNV:CalcPanelCoverage (NA17264_c_01_gDNA_01_B23H3TCLT3_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p NA17264_c_01_gDNA_01_B23H3TCLT3_1/
cnv_pipe calc-panel-coverage \
        NA17264_c_01_gDNA_01_B23H3TCLT3_1.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/NA17264_c_01_gDNA_01_B23H3TCLT3_1_counts.tsv \
        4 \
        20 \
        $(pwd)/NA17264_c_01_gDNA_01_B23H3TCLT3_1/