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What directory structure should subworkflow zip have?
I'm trying to run the workflow athttps://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline/blob/master/germline_single_sample_workflow.wdl on a v29 Cromwell server, but the input processing fails. I get the error:
Failed to import workflow ./unmapped_bam_to_aligned_bam.wdl.: File not found /tmp/4518464444991084952.zip3520711126153810536/tasks/unmapped_bam_to_aligned_bam.wdl File not found /unmapped_bam_to_aligned_bam.wdl unmapped_bam_to_aligned_bam.wdl: Name or service not known
The docs claim that the directory structure inside the zip should be the same as in the import statement: http://cromwell.readthedocs.io/en/develop/Imports/
My zip looks like this:
wm963-eb4:~/workspaces/five-dollar-genome-analysis-pipeline $ unzip -l tasks.zip Archive: tasks.zip Length Date Time Name --------- ---------- ----- ---- 0 02-16-2018 15:59 tasks/ 4793 02-15-2018 10:36 tasks/alignment.wdl 10530 02-15-2018 10:36 tasks/bam_processing.wdl 4399 02-15-2018 10:36 tasks/germline_variant_discovery.wdl 15156 02-15-2018 10:36 tasks/qc.wdl 6603 02-15-2018 10:36 tasks/utilities.wdl 19972 02-15-2018 10:36 unmapped_bam_to_aligned_bam.wdl --------- ------- 61453 7 files
My submit command is
curl -s -F [email protected]_single_sample_workflow.wdl -F [email protected]_single_sample_workflow.hg38.inputs.json -F [email protected] -F [email protected] https://cromwell-v29.dsde-methods.broadinstitute.org/api/workflows/v1
where options.json is empty and tasks.zip is as above.
If I move the unmapped_bam_to_aligned_bam.wdl into the tasks folder inside the zip, the error I get is for the next import:
Failed to import workflow tasks/germline_variant_discovery.wdl.: File not found /tmp/3009484190083449654.zip7335927595109280368/tasks/tasks/germline_variant_discovery.wdl File not found /tasks/germline_variant_discovery.wdl tasks%2Fgermline_variant_discovery.wdl: Name or service not known
The /tasks/tasks/ in the error above makes me think that Cromwell is creating a directory for the output of the zip, which is not what I was led to believe by the docs. What should the zip file structure look like for the import statements in this WDL?