Workflow Variables Rename Outputfile

#1

Hi,

I would like to rename the final outputs of my workflow with the name of the very first input file (input to the workflow at the beginning) and add some additional information.
I read the tutorial (https://galaxyproject.org/learn/advanced-workflow/variables/) and used #{input_name}_SnpEffAnnotation to rename the dataset. However the output file has the following filename now: “-SnpEffAnnotaiton”. (I also added two tags to the first input file #TST170_32a (which is the name of the first input file) and #originalannotation and delete the tag #originalannotation in the output of tool in the middle of the workflow and only kept #TST170_32a.)
Is there a possibility to not rename every output from every step of the workflow but just the output of the last tool and rename it to the name of the very first input to the workflow with some information added (e.g._SnpEffAnnotation).
Thanks for the help!
All the best,
Rose

Guidance on renaming datasets in workflows
#2

Hi Rose,
each step in a workflow only has access to its own inputs, so no, what you imagine is not possible.
You may try workflow parameters though: use ${name_of_your_choice} in the new output name (or anywhere else in the workflow) and this will create a workflow parameter (displayed in a small box in the upper right corner of the editor window).
You can reuse this parameter throughout the workflow and will be prompted to provide an actual value for it at the top of the workflow run dialogue.

1 Like
#3

Hi Wolfgang,

thanks a lot for your answer. Your option worked very well. If I understand you correct, there is no option to somehow keep the samplename throughout the process in order to not have to not down the sample names for each sample when running the workflow for various samples, is there? If not, no problem, then I will use the option you mentioned.

Thanks a lot!

All the best Rose