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We've been asked by CKCC and other projects to give a price-sheet for our services.  Over time we will update and refine our prices based on improved metadata collection and efficiency gains in the pipeline.  Our pricing based on current runtime/storage estimates is provided below.

Workflow & Tool Creation Service 

This service creates Docker-based tools described with CWL and registered in Dockstore and/or creates Toil workflows that use one or more Docker-based tools.  We have three options to support our customers for the creation of new tools and workflows.

 Research Project (John, Jacob, Arjun, and others)Core Authored (Jeltje)Consulting (Curoverse currently)
Cost"free"$150/hour$250/hour, complex workflows can cost in upwards of $5-$10K.
TimeBased on graduate student availability/PI's priorityLimited availability, based on current production workloadStarting at 2 weeks and increasing based on complexity.
AuthorGraduate students, postdocs, and researchers in the Genomic InstituteThe production staff of the core (Jeltje). Mainly focused on tool wrapping in Docker and testing workflows from researchers. Work is organized during the monthly steering committee meetings. Invoices will be provided.Third-party bioinformatics consulting, requires statement of work and consulting agreement.

To request a new workflow or tool be made available in the core please fill out the workflow/tool ordering form indicating a contact who we can work with, tool name, timeline, etc.

This is also a monthly (third Wednesday at noon) Analysis Core Steering Committee meeting where workflow priorities for the institute are discussed.  Contact Nicholas Theodosis ( to be added to the list.

We have currently partnered with Curoverse (hopefully more options to come) for their tool/workflow-creation consulting service.  This will be great if the core developers don't have bandwidth to service your tool/workflow request fast enough.  For those interested I can arrange for a quote, here's the information I need:

  • Code as a tarball or git repo
  • Sample inputs and known good output files for those inputs [intermediate files are a bonus]
  • Any standard concordance test, if relevant
  • The more documentation, the better

Workflow Execution Services (One Time Expenses)

The workflow execution service runs workflows designed to support a variety of experimental designs on AWS and/or Azure.  These are our current "production" workflows which means they represent the current best practices for the Analysis Core.  New workflows and new versions of existing workflows are regularly released. We will update pricing as appropriate.  For AWS we use spot instance pricing which means workflows may occasionally not be available (if the current market price exceeds the quoted amount below).  You can opt for "regular" instance pricing which is 10x greater but workflow requests will be executed in a non-interruptible fashion.  Each batch of samples carries a flat charge of $250 to cover the costs of setting up workflow runs and curating inputs so we highly recommend consolidating batches of workflow run requests whenever possible. We will provide credits for these batch prices for projects that provide direct support for core staff's salary. For more information about our in progress workflows see: Production Workflows  To request analysis please use our workflow analysis ordering form.

In the future we hope to offer Azure as an alternative to AWS since we can, essentially, offer free compute in this environment and storage is ~1/2 the price below. 

Self Executed Workflows 

We encourage any users of the core that are interested to run their own analysis to view our workflows on  We use the site as a redistribution point for our production workflows with our goal of redistributing all of our production pipelines via this platform.  This is a great option for running analysis via Docker locally (via the OpenStack environment at UCSC) and reducing compute expenses to virtually nothing.  However, there are pretty severe limits to the number of simultaneous workflows that are possible.  Generally, for <1 dozen workflow runs we suggest running them yourself via Docker.  For >1 dozen we recommend having the core run analysis at scale on AWS.

Another option we're actively working on is working with DNAStack, Seven Bridges, and other projects to provide execution services for our production workflows.  While their costs are likely to be higher than the core, they provide complete platforms with user interfaces that make it easy to organize files and share results with collaborators.  Look for announcements on as we integrate with these third-party genomics cloud platforms.

Core Executed Workflows on AWS

See Workflow Runtimes for how we calculated these prices.  We charge for spot compute + 1 month of storage.  If you want us to retain data after the first month we will charge the monthly fee:

See Production Workflows

PipelineVersionPricingStorage FootprintTotal (First Month Compute+Storage)
ProTECTbeta 1.0$8200GB$18 / sample
RNASeq-CGL2.1$450GB$6.50 / sample
Alignment (WES)2.1$2150GB$9.50 / sample
Exome Var (WES)2.1$7included in 150GB above$7 / sample
PCAWG Alignment (Somatic WGS)2.6.8$6300GB$21 / donor (N+T)
PCAWG Sanger Var (Somatic WGS)2.0.0$184GB$19 / donor (N+T)
PCAWG DKFZ/EMBL Var (Somatic WGS)2.0.0$135GB$14 / donor (N+T)

Data Storage Services (Recurring Monthly Expenses)

See Workflow Runtimes for how we calculated these prices.  We charge for spot compute + 1 month of storage when running the workflows.  After the first month, if we retain information on AWS we need to charge a monthly maintenance fee to maintain data on the cloud.  To avoid these charges please request a "cleanup".  Please be aware we can't be responsible for data not retained on AWS S3 e.g. data stored on the local POD infrasturcture.

Let us know if you expect multiple transfers of data out of AWS per month, we built in one transfer per month into the pricing below.

See Production Workflows

PipelineVersionStorage FootprintRecurring Monthy Storage Charge (After First Month)
ProTECTbeta 1.0200GB$10 (including one transfer out per month)
RNASeq-CGL2.150GB$2.50 (including one transfer out per month)
Alignment (WES)2.1150GB$7.50 (including one transfer out per month)
Exome Var (WES)2.15GB$1 (including one transfer out per month)
PCAWG Alignment (Somatic WGS)2.6.8300GB$15 (including one transfer out per month)
PCAWG Sanger Var (Somatic WGS)2.0.04GB$1 (including one transfer out per month)
PCAWG DKFZ/EMBL Var (Somatic WGS)2.0.05GB$1 (including one transfer out per month)

Order Now

Use the workflow analysis ordering form to place an order and we will contact you to discuss your needs.

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