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  1. yaml='
  2. name: sra_to_fastq
  3. description: Run fastq_dump file to generate fastq files from SRA files
  4. inputParameters:
  5. - name: INPUT
  6.   defaultValue: SRR1575914
  7. outputParameters:
  8. - name: OUTPUT
  9.   localCopy:
  10.     disk: datadisk
  11.     path: output/*
  12. resources:
  13.   minimumCpuCores: 1
  14.   minimumRamGb: 1
  15.   zones:
  16.   - us-central1-a
  17.   - us-central1-b
  18.   - us-central1-c
  19.   - us-central1-f
  20.   disks:
  21.   - name: datadisk
  22.     type: PERSISTENT_HDD
  23.     sizeGb: 100
  24.     mountPoint: /mnt/data
  25. docker:
  26.   imageName: actor0/bam2go'
  27.  
  28. sra_to_fastq(){
  29.   local input=$1
  30.   local output=$2
  31.   echo "$yaml" > ./$FUNCNAME.yaml
  32.   local cmd="
  33. gcloud alpha genomics pipelines run \
  34.   --pipeline-file ./$FUNCNAME.yaml \
  35.   --logging $output/logs \
  36.   --inputs INPUT=$input \
  37.   --outputs OUTPUT=$output"
  38.   echo "$cmd"
  39. }
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