If you are coming from a computer science background, you will notice that the definition is quite similar to a common understanding of the term “job” ( wikipedia). It represents a single run of a single tool found within a workflow. Job – this refers to the “execution” part from the “Task” definition (see above). Depending on what is being executed (tool or workflow), a single task can consist of only one tool execution (tool case) or multiple executions (one or more per each tool in the workflow). Task – represents an execution of a particular tool or workflow on the Platform. Workflow / Pipeline (interchangeably used) – denotes a number of tools connected together in order to perform multiple analysis steps in one run.Īpp stands for a CWL wrapper of a tool or a workflow that is created or already available on the Platform. Tool / App refers to a stand-alone bioinformatics tool or its Common Workflow Language (CWL) wrapper that is created or already available on the Platform. Based on internal knowledge and experience, the Seven Bridges team has come up with the Troubleshooting Cheat Sheet (Figure 1) which should help you navigate through the process of resolving the failed tasks. Even though there are a number of Platform features that help with tracking down the issues, the less-experienced users can still face challenges with troubleshooting because the whole process might assume familiarity digging through the tool and system messages.įortunately, there is a set of steps that most often brings us to the solution. However, one of the reasons for developing the Platform in the first place is to enable an additional level of abstraction between the users and low-level command line work in the terminal. This confidence usually comes with experience – the experience with bioinformatics tools and Linux environment in general, but also the experience with the Platform features. Often the first step to a user becoming comfortable using CGC is their gaining confidence in resolving issues they encounter on their own.
Tasks and examples described in this guide are available as a public project on the CGC. ↳ Data Browser query: start by searching for an ID.↳ Data Browser query: multiple dataset query.↳ Data Browser query: start from an existing query.↳ Data Browser query: start from scratch.
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