source '/cromwell_root/gcs_transfer.sh'

timestamped_message 'Localization script execution started...'



# Localize files from source bucket 'broad-institute-gdac' to container parent directory '/cromwell_root/broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome'.
files_to_localize_f0ae8412a159fdc5afd6813a2377cc0d=(
  "broad-firecloud-cptac"   # project to use if requester pays
  "3" # max transfer attempts
  "/cromwell_root/broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/" # container parent directory
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr15.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr18.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chrY.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr2.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr5.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr7.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr4.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr19.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr14.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr22.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr16.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr20.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr10.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr1.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr9.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr21.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chrX.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr17.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr6.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr12.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr3.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr8.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr13.txt"
  "gs://broad-institute-gdac/reference/genome/GRCh38.d1.vd1__by_chromosome/chr11.txt"
)

localize_files "${files_to_localize_f0ae8412a159fdc5afd6813a2377cc0d[@]}"
       



# Localize files from source bucket 'fc-fa05c490-b7c1-4ddd-ba57-cfae0646dc55' to container parent directory '/cromwell_root'.
files_to_localize_3592a4e6b1e6ebcd7c1e0307b7b5a1cf=(
  "broad-firecloud-cptac"   # project to use if requester pays
  "3" # max transfer attempts
  "/cromwell_root/" # container parent directory
  "gs://fc-fa05c490-b7c1-4ddd-ba57-cfae0646dc55/77737ddc-0d1f-4a06-9b24-163e4ec1c4ac/mutation_signature_analyzer_workflow/5bee7318-8a1c-49bb-9455-9abeca324d7f/call-mutation_signature_analyzer/script"
)

localize_files "${files_to_localize_3592a4e6b1e6ebcd7c1e0307b7b5a1cf[@]}"
       


# Localize files from source bucket 'fc-fa05c490-b7c1-4ddd-ba57-cfae0646dc55' to container parent directory '/cromwell_root/fc-fa05c490-b7c1-4ddd-ba57-cfae0646dc55/8d0a6ddf-d9de-450d-8efc-e64889401379/mutation_mutsig2cv/2023a925-d8e9-4535-bf4a-ed766f0a9a52/call-tool_mutsig2cv'.
files_to_localize_b07d7f29959a5d387ed47d2d66feda05=(
  "broad-firecloud-cptac"   # project to use if requester pays
  "3" # max transfer attempts
  "/cromwell_root/fc-fa05c490-b7c1-4ddd-ba57-cfae0646dc55/8d0a6ddf-d9de-450d-8efc-e64889401379/mutation_mutsig2cv/2023a925-d8e9-4535-bf4a-ed766f0a9a52/call-tool_mutsig2cv/" # container parent directory
  "gs://fc-fa05c490-b7c1-4ddd-ba57-cfae0646dc55/8d0a6ddf-d9de-450d-8efc-e64889401379/mutation_mutsig2cv/2023a925-d8e9-4535-bf4a-ed766f0a9a52/call-tool_mutsig2cv/CPTAC3-LSCC-v2.final_analysis_set.maf"
)

localize_files "${files_to_localize_b07d7f29959a5d387ed47d2d66feda05[@]}"
       
timestamped_message 'Localization script execution complete.'