.command.sh - Workdir - GERMLINE_CNV:CalcPanelCoverage (869_K08-N1-BDNA-1_B2377KTLT3_3)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/9d0da5f3aaf0739117d9d2bc2c0774/.command.sh
Size: 386 bytes
Task: GERMLINE_CNV:CalcPanelCoverage (869_K08-N1-BDNA-1_B2377KTLT3_3)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p 869_K08-N1-BDNA-1_B2377KTLT3_3/
cnv_pipe calc-panel-coverage \
        869_K08-N1-BDNA-1_B2377KTLT3_3.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/869_K08-N1-BDNA-1_B2377KTLT3_3_counts.tsv \
        4 \
        20 \
        $(pwd)/869_K08-N1-BDNA-1_B2377KTLT3_3/