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Question: renaming datasets in workflows, small probelm with Unified Genotyper and output_vcf
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gravatar for Guy Reeves
3.7 years ago by
Guy Reeves • 1.0k
Germany
Guy Reeves • 1.0k wrote:

Hi 

I have been successfully following the renaming datasets in workflows advice , it is very very useful capacity.

https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/VariablesEdit?action=show&redirect=Learn%2FAdvancedWorkflow%2FVariables

However I am having trouble renaming the outputs from 'Unified Genotyper'   

I am using the usegalaxy.org server

e.g.

'Rename Dataset on output_vcf

Available inputs are:reference_source|input_bams_0|input_bam, reference_source|ref_file'

 

However I have tried '#{input_bam | basename}_GENO'  and a number of other variations but cannot get it to take any information from the name of the single bam input file I am using.

Of all the tools I have used it is only 'Unified Genotyper'    and 'Plotting tool' that I have have had difficulty follwoing the advice on the above wiki page.

Any advice Thanks Guy
unified genotyper workflow plotting renaming • 913 views
ADD COMMENT • link •
modified 3.7 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.7 years ago by Guy Reeves • 1.0k
0
gravatar for Jennifer Hillman Jackson
3.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I was able to confirm this behavior yesterday. Our team is reviewing the issue. More details will be posted.

Thank you so much for reporting the issue! Jen, Galaxy team
ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k
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