Re: [galaxy-dev] New post action with workflows : DeleteIntermediatesActionOutput

2014-09-23 Thread Dannon Baker
Can you show me a screenshot or json output of the workflow? Situations where the delete intermediates action wouldn't delete a dataset are: 1) Subsequent job that has not finished still needs that dataset. 2) Dataset is marked as an output. 3) The job that creates the dataset isn't finished at t

Re: [galaxy-dev] New post action with workflows : DeleteIntermediatesActionOutput

2014-09-23 Thread julie dubois
OK!!! Thanks it's more clear for me. So I've a bug! I've followed your instructions. the DeleteAction is attached to the final step of my workflow. Before this, 2 steps exist with one output dataset not marked as output of workflow for each of this 2 step. The dataset of my first step is hidden and

Re: [galaxy-dev] New post action with workflows : DeleteIntermediatesActionOutput

2014-09-23 Thread Dannon Baker
Hi Julie, You don't attach the 'Delete Intermediate Datasets' action to a dataset you want to delete -- you attach it to one of the 'final' output steps of your workflow, at which point the action will clean up all datasets up to that point. So, for a simple example, see this workflow for selecti

Re: [galaxy-dev] New post action with workflows : DeleteIntermediatesActionOutput

2014-09-23 Thread julie dubois
Hi Dannon, Thanks for your answer. Sorry but I think I don't understand all of your explanations. First : if an output is marked with a highlighted snowflake, it will be not deleted : it's OK Second : if a dataset is used in several steps of my workflow, it will be deleted when all these steps wi

Re: [galaxy-dev] New post action with workflows : DeleteIntermediatesActionOutput

2014-09-23 Thread Dannon Baker
Hi Julie! The action resolves at the completion time of the job it is attached to, deleting datasets of any other already-completed jobs in that workflow which are not marked as an output step (with a highlighted snowflake). This will *not* delete datasets of any job marked as an output. Perhaps