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
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.
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.
I also tried to make a workflow and to make the final file to have the same name as the first input file, but I failed. I tries to input in the rename option on each tool #{input_name} or #{input} or #{input1}, but nothing hapens…
Did you already try the parameter method as wm75 advised?
Using group tags is another method that we’ve added in more recently. This doesn’t rename the dataset itself – but does keep track of all files associated with a particular sample, and does that through all steps. See Group tags for complex experimental designs
The rename feature works for me on EU (v 23.1).
You need to make sure, that you use exactly the var name proposed.
Here is an Example:
In the workflow renaming fastQC output based on the input, using the basename:
Output will be (#4):
Keep in mind that this will rename the collection, not the elements in the collection.
But it also works for single file (#17):
But unfortunately if you have an extension such as bla.fastq.gz; the base name will be bla.fastq … this is not ideal. But still, the file name can be used as var.
Note: the other syntax with the $ sign is indeed no longer supported since workflow variables have been replaced with workflow input parameters (see the following screenshot of the Inputs section of the workflow editor tools bar.
