c3 or just 3 should work assuming a recent version of Galaxy (and the input dataset in question having at least 3 columns). which galaxy server are you working on, and can you send a bug report using the bug icon?
I suspected that when I used the tool directly (not using the tool via Workflow), the Count tool has to recognize or read the data first so it can know how many columns there are in the data. When i open the tool and not selecting any data, it showed this
If this is the case, does it mean that this tool could not work in Workflow? because it cannot know beforehand how many columns are going to be in the data? (My SAM data is generated in the middle of my Workflow)
I created a small workflow replicating your descriptions, and it seems to work whether the SAM header is included or not. The output with a header is noisier. Maybe this will help? Both the history and the workflow can be imported, reviewed, and compared to what you have now. You might also want to apply the “workflow metadata reset” below – now while troubleshooting this tool, then later as needed.
Tip: Workflow metadata “reset”: When upstream inputs or steps have certain changes applied during editing (data structure, metadata), it can help to disconnect all of the “noodles” between downstream steps, then to reconnect again in the order of execution.