.command.sh - Workdir - GERMLINE_CNV:CalcPanelCoverage (NCI-BL2122_c_01_gDNA_0001_A237FLHLT3_2)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5a/4e0260b1ec500759d2abf88e89e08e/.command.sh
Size: 418 bytes
Task: GERMLINE_CNV:CalcPanelCoverage (NCI-BL2122_c_01_gDNA_0001_A237FLHLT3_2)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p NCI-BL2122_c_01_gDNA_0001_A237FLHLT3_2/
cnv_pipe calc-panel-coverage \
        NCI-BL2122_c_01_gDNA_0001_A237FLHLT3_2.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/NCI-BL2122_c_01_gDNA_0001_A237FLHLT3_2_counts.tsv \
        4 \
        20 \
        $(pwd)/NCI-BL2122_c_01_gDNA_0001_A237FLHLT3_2/