gcloud run pipeline for bwa.bash

# Set according to your working enviroment
BUCKET=gs://your-bucket-name
WORKSPACE=$BUCKET/some/subdirectory
BASE_FASTA=some.fa
INPUT_FASTA=$BUCKET/$BASE_FASTA
# probably you want this to be the same as input.fasta.
# this is the default behavior for BWA.
OUTPUT_INDEX_PREFIX=$BASE_FASTA
OUTPUT_PATH=$WORKSPACE/out

gcloud alpha genomics pipelines run                                   \
  --pipeline-file pipeline-bwa.yaml                                   \
  --logging $WORKSPACE/log                                            \
  --inputs INPUT_FILE=$INPUT_FASTA,OUTPUT_INDEX_PREFIX=$OUTPUT_PREFIX \
  --outputs OUTPUT_PATH=$OUTPUT_PATH