.command.sh - Workdir - CNV_PIPE:CalcPanelCoverage (FC13_cnv_mosaic_calc_panel_coverage_3619658683_r13)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/8ac474886da8a659de4793eb680784/.command.sh
Size: 320 bytes
Task: CNV_PIPE:CalcPanelCoverage (FC13_cnv_mosaic_calc_panel_coverage_3619658683_r13)
Attempt

Content

#!/bin/bash -Ceuo pipefail
echo "$(pwd)"
mkdir  -p 3619658683_r13/
cnv_pipe calc-panel-coverage \
        3619658683_r13.bam \
        Renasight_CNV.mosatic.tm.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/counts.tsv \
        1 \
        20 \
        $(pwd)/3619658683_r13/ \