Multi sample processing workflow


I am new to KNIME and started reading some documentation. My understanding now is, that I can create a workflow which is supposed to process an input or maybe a given set of inputs. Which means that this is kind of a fixed/static set. There is one point I haven't understood yet,  How do you cope with multiple samples ?

For example: Lets assume there are a number of input files comming from a different sample each, like SampleA, SampleB, etc. In case of there is no interaction, (like: at some processing stage all samples needed to be processed together) than there is no problem: I would just run my workflow for each sample separately, one by one. However, if there is some kind of interaction, is it possible

  1. to model a node which process all samples at once ? (... which means the node knows only at the time of runtime (or maybe while compilation of workflow together with inputs), how many inputs it gets.)
  2. to let the workflow run with an arbitrary number of samples at once ?

You understand what I mean ? Thanks for your help,


Dear Marian,

this depends on the node. We have different nodes which can handle multiple columns at once. And most of these can handle varying column names. 

However all of our nodes process multiple samples at once, as long as the column names stay the same.

Does this cover your question? 

Best regards, Iris

Hello Marian,

This is possible with a List Files node. You put all your input files into a directory which you set in the List Files node. Than use the Iterate List of Files node to read all files in. Now you have an arbitrary number of input files. For the further processing you can use a Group Loop to process one file at the time. If the files need different processing steps, you need some Switches to determine the the right process for each file.

As you have all samples in your workflow, you can of course use interactions as well, use Splitters and Concatenate to get divide your data and put it together later on.

Does this solve your problem?