Reputation: 63
I am trying to run the GATK best practices pipeline in google cloud and get below error
here's the gcloud command:
gcloud alpha genomics pipelines run \
--pipeline-file wdl_pipeline.yaml \
--regions us-central1 \
--inputs-from-file WDL=${GATK_GOOGLE_DIR}/PairedEndSingleSampleWf.gatk4.0.wdl,\
WORKFLOW_INPUTS=${GATK_GOOGLE_DIR}/PairedEndSingleSampleWf.hg38.inputs.json,\
WORKFLOW_OPTIONS=${GATK_GOOGLE_DIR}/PairedEndSingleSampleWf.gatk4.0.options.json \
--env-vars WORKSPACE=${GATK_OUTPUT_DIR}/work,\
OUTPUTS=${GATK_OUTPUT_DIR}/output \
--logging ${GATK_OUTPUT_DIR}/logging/
ERROR: (gcloud.alpha.genomics.pipelines.run) Unable to read file [wdl_pipeline.yaml]: [Errno 2] No such file or directory: 'wdl_pipeline.yaml'
Upvotes: 0
Views: 66
Reputation: 11
[UPDATE] The WDL Runner repository location had changed. The tutorial at https://cloud.google.com/genomics/docs/tutorials/gatk has been updated.
[ORIGINAL] If you're following the tutorial at https://cloud.google.com/genomics/docs/tutorials/gatk make sure to do step 4 where you change directories. It is telling you that the wdl file is not in the directory where you are.
Upvotes: 0