Run analysis steps
Cohesive's run analysis system is subdivided into 3 steps:
- Samples (sample selection);
- Tools (selection of the analysis type and bioinformatic tool);
- Inputs (input selection).
Please consider consulting the "Run analyses" Wiki page for an introduction and quick guide on the whole process.
This Wiki page debates how to go through the 3 steps "Samples", "Tools" and "Inputs".
Step 1: Samples
In order to be able to choose an analysis to perform, the system requires a collection of sample codes. Such collection will be used to request an analysis run on the appropriate input file associated to each of the desired samples.
The user can choose either the cart or a tag to provide the collection of codes. A tag is an immutable sample code collection, created and saved by the user. The cart is a transient and dynamic code collection system, built by the user, which can be also used as a filter by .
When using the cart to run an analysis, cart activation takes place automatically, overriding any active tag. Cart deactivation willtake back the Information System to the condition prior to cart activation.
If the cart contains no sample codes and there is no active tag, the links in the page will allow to quickly rectify that by leading the user to the appropriate pages.
In the page the user can also find a "Load utilities" function, which allows to perform a quick fill up of the cart, using a list of codes or a CSV file.
The short video below demonstrates the workflow of the sample selection step.
Step 2: Tools
The step "Tools" provides an interface to choose the desired analysis or pipeline and the bioinformatic tool to perform it. All available analyses are listed as buttons with pertinent information and can be filtered by category.
After analysis selection, the user will be able to select the chosen bioinformatic tool among those available. The following short video shows how to perform selection of analysis and tool.
Step 3: Inputs
To complete the run analysis process, it's necessary to specify what files, associated with the sample codes, is expected as input for the selected bioinformatic software. As an example, trimming analysis requires the samples' raw reads, cgMLST performed with chewBBACA uses assembly fasta as input, while GrapeTree needs tabular files from cgMLST.
This step requires that all the necessary files have been produced and imported, (for example, it's not possible to run GrapeTree if chewBBACA has not been executed on the requested samples).
Usually at this stage the fields are pre-filled with the appropriate input and options for the selected tool, so action from the user will have to be taken only in case of multiple suitable inputs or if specific options are available. It is also possible to activate the advanced mode to select inputs.
The short video below shows how to select inputs for an analysis run.
Inputs: advanced mode
In some cases, inputs have to be managed in a way that allows to use files coming from different sources, for the same kind of analysis. To do that, the last run analysis step provides a switch to toggle between the "Base mode" and the "Advanced mode" for input selection, the latter of which allows to choose multiple input types using checkboxes.
The following short video demonstrates the "Advanced mode" for input selection for one of the tools for which such mode is available: the CFSAN pipeline.
Selection of multiple references
Some analyses (notably mapping with Ivar or pipelines that include it), can use more than one reference file. Reference selection can be performed by opening the reference genomes pop-up window and selecting any of them through the coresponding checkboxes. Repeating the process will not overwrite references selected previously: the new references will be concatenated to the end of the list.
The list of selected references can be cleaned, ordered, or single references can be removed one by one.
Nota: reference order impacts on the final outcome of the multi-reference mapping. Please order the main references first.
The following videotutorial demonstrates how to interact with options for selection of multiple references.
