Download WDL and inputs.json from Firecloud
mooses
Member ✭
Hi,
I'd like to download a project from Firecloud and run it locally:
https://portal.firecloud.org/#workspaces/help-gatk/Germline-SNPs-Indels-GATK4-b37
Is there a way to download the whole WDL + inputs.json package as e.g. zip?
Thanks!
Best Answer
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abaumann
Broad DSDE ✭✭✭
Unfortunately there is not a way to do this via UI or API easily, however you can do this:
To get the WDL, you can call this, just replace the parts inside the with your own information
curl -H "Authorization:Bearer $(gcloud auth print-access-token)" https://api.firecloud.org/api/workspaces/<your workspace's project>/<your workspace name>/submissions/<your submission id>/workflows/<your workflow id> | jq -r ".submittedFiles.workflow" > name_of_the_wdl_you_want.wdlTo get the inputs:
curl -H "Authorization:Bearer $(gcloud auth print-access-token)" https://api.firecloud.org/api/workspaces/<your workspace's project>/<your workspace name>/submissions/<your submission id>/workflows/<your workflow id> | jq -r ".submittedFiles.inputs" > name_of_the_inputs_file_you_want.inputs
Answers
Unfortunately there is not a way to do this via UI or API easily, however you can do this:
To get the WDL, you can call this, just replace the parts inside the with your own information
curl -H "Authorization:Bearer $(gcloud auth print-access-token)" https://api.firecloud.org/api/workspaces/<your workspace's project>/<your workspace name>/submissions/<your submission id>/workflows/<your workflow id> | jq -r ".submittedFiles.workflow" > name_of_the_wdl_you_want.wdlTo get the inputs:
curl -H "Authorization:Bearer $(gcloud auth print-access-token)" https://api.firecloud.org/api/workspaces/<your workspace's project>/<your workspace name>/submissions/<your submission id>/workflows/<your workflow id> | jq -r ".submittedFiles.inputs" > name_of_the_inputs_file_you_want.inputsOk, thanks!
Any chance of sharing this on GitHub:
https://portal.firecloud.org/#workspaces/help-gatk/Germline-SNPs-Indels-GATK4-b37
No problem!
What do you mean by sharing a workspace on github?
Hi,
I'm asking if you would be able to share the Germline-SNPs-Indels-GATK4-b37 project for collaboration on GitHub. So a project such as this:
https://github.com/gatk-workflows/five-dollar-genome-analysis-pipeline.
On FireCloud, I can see the sub-workflows of this workflow:
https://portal.firecloud.org/#workspaces/help-gatk/Germline-SNPs-Indels-GATK4-b37/method-configs
But I'm not able to find:
Am I just not looking at the correct tab or are they not available on the portal?
Thanks.
I think what you want is here:
https://github.com/gatk-workflows/gatk4-germline-snps-indels ?
and you can find others in the root https://github.com/gatk-workflows
Ok, this looks good! So does it work with b37 reference as well?
That I don't know the answer to - I'll ask someone else on the forum to answer that
This also seems to be missing the processing-for-variant-discovery-gatk4 workflow available on Firecloud:
https://portal.firecloud.org/#workspaces/help-gatk/Germline-SNPs-Indels-GATK4-b37/method-configs
Yes it works with b37. If look at the methods in the hg38 and b37 workspace you'll see they are using the same method. They are just using different reference files within their respective workspace.
You'll find the processing-for-variant-discovery-gatk4 workflow here :
https://github.com/gatk-workflows/gatk4-data-processing
Like abaumann mentioned you'll find many of the workflows links in
https://github.com/gatk-workflows