Question: Naming Files Automatically
gravatar for mccoykg
3.4 years ago by
United States
mccoykg80 wrote:

Hi all. I'm creating a workflow that uses input files named by their barcodes, and I'd like to know if there's a way to automatically "pass on" the barcodes to the names of outputs further down in the workflow. For example, if the workflow were just clipping the files then mapping them, I'd like the resulting map files to be named by the same barcode as the original input file. I know there's a "Rename Dataset on output" option, but since I'll be running these in batch - with potentially hundreds of barcodes in the future - entering the barcodes and running the workflow by hand for each one isn't very practical.

I'd like to do this so that I can distinguish between all the different outputs created when analyzing the many files resulting from barcode splitting. Has anyone run into this problem, or found an alternative way to distinguish between many outputs, besides renaming them manually one by one? Thanks much for any help.

barcode splitter naming • 877 views
ADD COMMENTlink modified 3.4 years ago by Guy Reeves1.0k • written 3.4 years ago by mccoykg80
gravatar for Bjoern Gruening
3.4 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:


please have a look at this site I hope this will help you! Sorry we are all quite busy preparing for the Galaxy Community Conference next week.



ADD COMMENTlink written 3.4 years ago by Bjoern Gruening5.1k

This was very helpful. If anyone is having a similar problem, I managed to get my files named by their barcodes by splitting my workflow into two parts; the first part ends on the barcode splitter tool, and the second part runs as a batch job where each file is named by the base of its input + the file type.

ADD REPLYlink written 3.4 years ago by mccoykg80
gravatar for Guy Reeves
3.4 years ago by
Guy Reeves1.0k
Guy Reeves1.0k wrote:



​I think this question or variants of it appear fairly regularly here, while  they are already among the most up- voted posts, if you also up-vote them maybe this will encourage additional developments in this general area.

C: Creating a Workflow for Variant Detection for 200 samples

Adding read group information in a bam header

Is it possible for workflow parameters to take information from the names of input datasets? e.g. ${Read_group } is set to be the first three characters of input dataset name.

Thanks  Guy




ADD COMMENTlink written 3.4 years ago by Guy Reeves1.0k

Thanks, I'll do that! It seems like a really useful - and kind of intuitive - feature to include.

ADD REPLYlink written 3.4 years ago by mccoykg80
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