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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'

Sangam Belose
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Sethuramalingam Sundaram
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1 Answers1

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[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.

a m
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  • Thanks for the response, Not able to locate the git folder "https://github.com/openwdl/wdl/tree/master/runners/cromwell_on_google.git" which should have the file. – Sethuramalingam Sundaram Feb 07 '19 at 17:44
  • Looks like that repo has been moved to https://github.com/broadinstitute/wdl-runner Replace the original git clone ... openwdl with: git clone https://github.com/broadinstitute/wdl-runner.git And then in Step 4, change the command to be: cd wdl-runner/wdl_runner Will work on updating the tutorial. Thanks. – a m Feb 08 '19 at 18:30
  • @SethuramalingamSundaram If this is resolved now, could you please mark it as fixed – a m Feb 21 '19 at 22:59