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Copy path2021-12-07_haley_migrate_qa_files.sh
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2021-12-07_haley_migrate_qa_files.sh
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# Description: move all old QA files to archive folder and generate new QA log files for each cohort.
# Author: Haley Hunter-Zinck
# Date: 2021-12-07
#########################
# parameters #
#########################
synid_folder_archive=syn26529519
synid_folder_brca=syn25872288
synid_folder_crc=syn25878117
synid_folder_nsclc=syn25872287
synid_folder_panc=syn25882184
synid_folder_prostate=syn25976290
#########################
# migrate old QA files #
#########################
synapse create -parentid syn25832316 -name archive Folder
# BrCa
synapse list $synid_folder_brca > res.txt
for synid in $(cut -f 1 -d ' ' res.txt)
{
synapse mv --id $synid --parentid $synid_folder_archive
}
# CRC
synapse list $synid_folder_crc > res.txt
for synid in $(cut -f 1 -d ' ' res.txt)
{
synapse mv --id $synid --parentid $synid_folder_archive
}
# NSCLC
synapse list $synid_folder_nsclc > res.txt
for synid in $(cut -f 1 -d ' ' res.txt)
{
synapse mv --id $synid --parentid $synid_folder_archive
}
# PANC
synapse list $synid_folder_panc > res.txt
for synid in $(cut -f 1 -d ' ' res.txt)
{
synapse mv --id $synid --parentid $synid_folder_archive
}
# prostate
synapse list $synid_folder_prostate > res.txt
for synid in $(cut -f 1 -d ' ' res.txt)
{
synapse mv --id $synid --parentid $synid_folder_archive
}
#########################
# generate new QA files #
#########################
# BrCa
for level in error warning
{
for site in DFCI MSK VICC
{
Rscript main.R -c BrCa -s $site -r upload -l $level -v -u $synid_folder_brca
}
Rscript main.R -c BrCa -s all -r table -l $level -v -u $synid_folder_brca
Rscript main.R -c BrCa -s all -r comparison -l $level -v -u $synid_folder_brca
}
# CRC
for level in error warning
{
for site in DFCI MSK VICC
{
Rscript main.R -c CRC -s $site -r upload -l $level -v -u $synid_folder_crc
}
Rscript main.R -c CRC -s all -r table -l $level -v -u $synid_folder_crc
Rscript main.R -c CRC -s all -r comparison -l $level -v -u $synid_folder_crc
Rscript main.R -c CRC -s all -r release -l error -v -u $synid_folder_crc
}
# NSCLC
for level in error warning
{
for site in DFCI MSK UHN VICC
{
Rscript main.R -c NSCLC -s $site -r upload -l $level -v -u $synid_folder_nsclc
}
Rscript main.R -c NSCLC -s all -r table -l $level -v -u $synid_folder_nsclc
Rscript main.R -c NSCLC -s all -r comparison -l $level -v -u $synid_folder_nsclc
Rscript main.R -c NSCLC -s all -r release -l error -v -u $synid_folder_nsclc
}
# PANC
for level in error warning
{
for site in DFCI MSK UHN VICC
{
Rscript main.R -c PANC -s $site -r upload -l $level -v -u $synid_folder_panc
}
Rscript main.R -c PANC -s all -r table -l $level -v -u $synid_folder_panc
Rscript main.R -c PANC -s all -r comparison -l $level -v -u $synid_folder_panc
}
# Prostate
for level in error warning
{
for site in DFCI MSK UHN VICC
{
Rscript main.R -c Prostate -s $site -r upload -l $level -v -u $synid_folder_prostate
}
Rscript main.R -c Prostate -s all -r table -l $level -v -u $synid_folder_prostate
Rscript main.R -c Prostate -s all -r comparison -l $level -v -u $synid_folder_prostate
}