cram2fastq

Takes a CRAM URL, converts to FASTQ and uploads to GCS bucket.

Running in Kubernetes

Execute

cram2fastq_k8 run <gcp-user-project> <cram-url> <output-bucket> <sample-name>

Example HMF

# execute
cram2fastq_k8 run "hmf-crunch" "gs://hmf-cram2fastq/cram/CPCT12345678T.cram" "hmf-cram2fastq" "CPCT12345678R"

# output will then be in
gs://hmf-cram2fastq/CPCT12345678T_FASTQ

Monitoring

kubectl get jobs | grep cram2f
kubectl get pods | grep cram2f
kubectl logs <pod-name>