.command.sh - Workdir - GERMLINE_CNV:CalcPanelCoverage (1029_BQ3K-N1-BDNA-1_B23K7JFLT3_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/5f8840f9cb67720c7ed96e080ea736/.command.sh
Size: 394 bytes
Task: GERMLINE_CNV:CalcPanelCoverage (1029_BQ3K-N1-BDNA-1_B23K7JFLT3_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p 1029_BQ3K-N1-BDNA-1_B23K7JFLT3_1/
cnv_pipe calc-panel-coverage \
        1029_BQ3K-N1-BDNA-1_B23K7JFLT3_1.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/1029_BQ3K-N1-BDNA-1_B23K7JFLT3_1_counts.tsv \
        4 \
        20 \
        $(pwd)/1029_BQ3K-N1-BDNA-1_B23K7JFLT3_1/