CODEWITHSUNDEEP
google-genomics
Sethuramalingam Sundaram
Sethuramalingam Sundaram

Reputation: 63

gcloud.alpha.genomics.pipelines.run - No such file or directory: 'wdl_pipeline.yaml'

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

Answers (1)

a m
a m

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

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