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More about running fastq-to-gvcf » History » Version 2

Peter Amstutz, 04/09/2025 03:30 PM

1 2 Peter Amstutz 
h1. More about running fastq-to-gVCF
2 1 Peter Amstutz 





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When we do releases, we run a test pipeline that is intended to be representative of a bioinformatics workload.





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1. Deploy the version of @arvados-cwl-runner@ that you want to test and make sure that the corresponding @arvados/jobs@ image "has been built and uploaded to docker hub":https://ci.arvados.org/view/Release%20Pipeline/job/docker-jobs-image-release/ or built using the @arvados/build/build-dev-docker-jobs-image.sh@ script and uploaded using @arv-keepdocker@.





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2. Clone https://git.arvados.org/arvados-tutorial.git/





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3. Create an Arvados project for the test run





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4. @cd arvados/tutorial/WGS-processing@





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5. Run the following command: @arvados-cwl-runner --no-wait --disable-reuse --project-uuid <my project> cwl/wgs-processing-wf.cwl yml/wgs-processing-wf-chr19.yml@





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6. Monitor this for success.  It usually takes about an hour to run.





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If you are running this on @pirca@ then all the data should already be present.  If you are running it from somewhere else, you may need to do some additional data copying from @pirca@ to the other cluster.  The input document @yml/wgs-processing-wf-chr19.yml@ has the portable data hashes of the collections.