.command.sh - Workdir - CNV_PIPE:MakeVCFsProbeMerge (FC13_cnv_mosaic_cnv_pipe_3574258956_r13_make_vcfs_probe)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/194bdbf4461a78047bc7b7d51aa1ea/.command.sh
Size: 427 bytes
Task: CNV_PIPE:MakeVCFsProbeMerge (FC13_cnv_mosaic_cnv_pipe_3574258956_r13_make_vcfs_probe)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p vcfs/
cnv_pipe make-probe-merged-vcfs \
    FC13_cnv_mosaic_4__probe_sample.parquet \
    ploidy_4.parquet \
    clustered_panel.csv \
    GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
    vcfs/  \
    1 \
    3574258956_r13 \
    --cutoff-json zscore_v1.json
mv vcfs/cnv_call_summary.tsv vcfs/cnv_call_3574258956_r13.tsv
mv vcfs/cnv_gene_summary.tsv vcfs/cnv_gene_3574258956_r13.tsv