Question: Variable doesn't work in Workflow editor for certain tools?
gravatar for vladimir.gritsenko
13 months ago by
Tel Aviv University
vladimir.gritsenko90 wrote:


I've started using variables in the workflow editor to make tracking the datasets easier, and so far its been working OK. One tool has given me trouble, though - UnifiedGenotyper. The BAM input name seems to be stored in the input_bam variable, but when I set the new dataset's name to #{input_bam} - extra text the variable resolves to an empty string. This tool has another varaible, ref_file (which references the name of the FASTA reference file), and that one works. I tried it a number of time, so relatively sure it's not just a typo on my part.

Thanks for any help!

workflow • 397 views
ADD COMMENTlink modified 13 months ago by Jennifer Hillman Jackson24k • written 13 months ago by vladimir.gritsenko90
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson24k wrote:


Yes, this is a possible outcome for certain tools. In particular, if using GATK tools at, the wrappers are deprecated and the underlying GATK tools are older (version 1.4). These will not be undergoing further development/tuning and will be at some point removed from the server entirely.

Using GATK in a local or cloud Galaxy, with the latest wrapper/tool versions, is recommended. Should you run into problems with these, create an issue against the Github development repository for the tool describing the unexpected behavior. A link to that can be found on the tool's home page in the Tool Shed.


ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson24k

Thanks for the reply! Is there a particular reason why you're phasing out these Broad tools? Aren't they considered best-of-breed for SNP calling? Does that mean you're recommending FreeBayes and VarScan for that purpose?

ADD REPLYlink written 13 months ago by vladimir.gritsenko90

The licensing for GATK is the issue. There are several alternatives in the tool group "NGS: Variant Analysis" at - including Freebayes. This has been discussed in other posts, for example:

Follow the 101 Tutorials here (includes an example using Freebayes):

Full 101 help is here:

ADD REPLYlink written 13 months ago by Jennifer Hillman Jackson24k
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