Hi all, I'm trying to update one of my saved workflows which was created using an old version of the filter tool BEFORE this tool had the option "Number of header lines to skip". In order to get rid of the nag message on using the tool, I want to re-save the workflow using the default 0 for this. This missing parameter was also causing problems trying to import the *.ga file for this old workflow, http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016223.html The (now out of date) copy of the Workflow is on the Tool Shed, but to update it I am working on the same Galaxy instance used to create it (where TMHMM and SignalP were manually installed and have been updated since): http://toolshed.g2.bx.psu.edu/view/peterjc/secreted_protein_workflow 1. Log into Galaxy 2. Click on workflows (top menu) 3. Find my workflow, select "Edit" from the dropdown menu 4. Observe warning: Workflow loaded with changes Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save. Step 3: Filter No value found for 'Number of header lines to skip', used default Step 6: Filter No value found for 'Number of header lines to skip', used default 5. Click on these workflow steps, verify this new parameter is set to zero. 6. Save the workflow, observe blue progress bar pops up. 7. Close the workflow 9. Save the workflow to disk as a *.ga file 8. Open the workflow again for editing Expected result: New parameter recorded, and tool versions updated. Actual result: No change, same warning appears. No sign of the new setting in the freshly save *.ga file. Tool versions not changed. Workaround: Change the default values to one ("1"), save, close, reopen, no warning, change values back to zero ("0"), save, close, reopen, Happy. Is this simply a bug where the workflow editor wrongly assumes no changes have been made (despite there being two major types of change - the new header_lines parameter, and the versions of the tools)? Peter