.command.sh - Workdir - CNV_PIPE:AggregateBatchData (FC13_cnv_mosaic_cnv_pipe_1_agg_batch)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/0a401cc23c89250d388893bd4859f6/.command.sh
Size: 818 bytes
Task: CNV_PIPE:AggregateBatchData (FC13_cnv_mosaic_cnv_pipe_1_agg_batch)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p clusters_1
copy_path.py folder s3://natera-platform-sandbox/platform-users/bding/CNV/FC13/CNV_working_Mosaic_v4_11/clusters_1/ clusters_1/clusters/
copy_path.py file s3://natera-platform-sandbox/platform-users/bding/CNV/FC13/CNV_working_Mosaic_v4_11/counts_1.parquet clusters_1/counts.parquet 
copy_path.py file s3://natera-platform-sandbox/platform-users/bding/CNV/FC13/CNV_working_Mosaic_v4_11/sample_metrics_1.parquet clusters_1/sample_metrics.parquet 
copy_path.py file s3://natera-platform-sandbox/platform-users/bding/CNV/FC13/CNV_working_Mosaic_v4_11/ploidy_1.parquet clusters_1/ploidy.parquet 
cnv_pipe aggregate-batch-data \
         ./clusters_1/ \
         Renasight_CNV.mosatic.tm.bed \
         renasight_blacklist_probes.bed \
         ./ \
         FC13_cnv_mosaic_1