.command.sh - Workdir - GERMLINE_CNV:CalcPanelCoverage (HG03267_c_0001_gDNA_0001_B23H2H2LT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/93cfa32b602b6ba3e3847e56ab49c4/.command.sh
Size: 414 bytes
Task: GERMLINE_CNV:CalcPanelCoverage (HG03267_c_0001_gDNA_0001_B23H2H2LT4_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p HG03267_c_0001_gDNA_0001_B23H2H2LT4_1/
cnv_pipe calc-panel-coverage \
        HG03267_c_0001_gDNA_0001_B23H2H2LT4_1.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/HG03267_c_0001_gDNA_0001_B23H2H2LT4_1_counts.tsv \
        4 \
        20 \
        $(pwd)/HG03267_c_0001_gDNA_0001_B23H2H2LT4_1/