Hi everyone,
I am creating a workflow in Galaxy that I will be using for variant analysis for about 200 samples. I have just hit another road block and I'm hoping someone can help. After I run BWA, I use the output (a BAM file) to generate a pileup. From here I would like to filter and concatenate the datasets. My problem is, the pileup does not include a column for sample name. I tried to use the tool "Add column" under Text Manipulation but this can only be assigned manually. I attempted to use the variable #{input name} in this field in hopes that this could dynamically add the correct sample name to the column as samples were processed in the workflow. Instead, the tool doesn't behave as I hoped and does not recognize this variable and this added column reads "input" for every sample processed. Any advice or suggestions would be appreciated.
