Question: FreeBayes doesn't use workflow variable
2
gravatar for szeplaki.bence
6 months ago by
szeplaki.bence30 wrote:

Hi,

I have a local Galaxy instance, and have made a workflow for multiple samples. The workflow works as intended, but I can't keep the names of the samples, because I lose them at the FreeBayes step. I could set the workflow variables, to keep filename of the previous step, except for FreeBayes.

I tried to use #{ input_bams } as input_bams is the name of the input file, but it didn't work. I also tried #{ reference_source|batchmode|input_bams} as it's the example for valid input, still, didn't work(I also tried a bunch of other variation of these). I run the FreeBayes in individual mode.

All the other used tools in the workflow modify the output filename according to my intentions, except for this one. It only give that generic name: 'FreeBayes on data N, data N, and data N'

I don't know if the workflow variable is broken for this one, or I just don't know the proper syntax.

FreeBayes version: 1.1.0.46-0 under Galaxy version: 18.01

Thanks in advance Bence

workflow variable freebayes • 403 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 6 months ago by szeplaki.bence30
1

I haven't tested this function with Freebayes specifically for some time. Doing so now. More feedback soon. Jen, Galaxy team

ADD REPLYlink written 6 months ago by Jennifer Hillman Jackson25k

Thanks for the response, have you found out something? Is something wrong with the wrapper? Or how can I properly set the output name, let's say the same as the input name?

ADD REPLYlink written 6 months ago by szeplaki.bence30
1

Testing still in progress. This is likely a tool problem but I'll confirm that.

ADD REPLYlink written 6 months ago by Jennifer Hillman Jackson25k
1

Hi, Jen Just checking in for updates on the testing. Thank you for all the efforts!

ADD REPLYlink written 5 months ago by szeplaki.bence30
2
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Update 6/4/2018

Hi - I haven't been able to get a successful run. Tried again today, no luck. I put the testing details into your Github ticket and pinged a developer who should be able to help. Let's track this there going forward. https://github.com/galaxyproject/tools-iuc/issues/1880

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k
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