.command.sh - Workdir - CNV_PIPE:AggregateBatchData (FC13_cnv_mosaic_cnv_pipe_2_agg_batch)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/427cb70965abc3aff968d01e9e2d0a/.command.sh
Size: 818 bytes
Task: CNV_PIPE:AggregateBatchData (FC13_cnv_mosaic_cnv_pipe_2_agg_batch)
Attempt

Content

#!/bin/bash -Ceuo pipefail
mkdir -p clusters_2
copy_path.py folder s3://natera-platform-sandbox/platform-users/bding/CNV/FC13/CNV_working_Mosaic_v4_11/clusters_2/ clusters_2/clusters/
copy_path.py file s3://natera-platform-sandbox/platform-users/bding/CNV/FC13/CNV_working_Mosaic_v4_11/counts_2.parquet clusters_2/counts.parquet 
copy_path.py file s3://natera-platform-sandbox/platform-users/bding/CNV/FC13/CNV_working_Mosaic_v4_11/sample_metrics_2.parquet clusters_2/sample_metrics.parquet 
copy_path.py file s3://natera-platform-sandbox/platform-users/bding/CNV/FC13/CNV_working_Mosaic_v4_11/ploidy_2.parquet clusters_2/ploidy.parquet 
cnv_pipe aggregate-batch-data \
         ./clusters_2/ \
         Renasight_CNV.mosatic.tm.bed \
         renasight_blacklist_probes.bed \
         ./ \
         FC13_cnv_mosaic_2