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NCI-CGR / IlluminaSequencingAnalysis

All Illumina Sequencing Related project from Xin will be recorded in this repo
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Customized QC: Get data from S3 back to network storage system (biowulf) #27

Open lxwgcool opened 3 years ago

lxwgcool commented 3 years ago

Using obj_get

file="lix33/COVID19/USU/Data/06_30_2021/ProcessedData/202107_XXXXXX_XXXX_H3NGNDSX2/BAM/BWA/v38/I3-97794_CTTGGTAT-GGACTTGG_L001_HQ_paired_dedup_nophix.bai"

obj_get -v DCEG_COVID_WGS  ${file} -D ./ -p -V --strip 6 --dry-run
lxwgcool commented 3 years ago

Get all csv from S3 to Biowulf

obj_ls -v DCEG_COVID_WGS -h -m "*.csv" | awk 'NR>1 {print $8}' | while read line; do obj_get -v DCEG_COVID_WGS ${line} -D ./ -p -V --strip 6 --dry-run; done