Question: Parallelism with Multiple Outputs : HOW?
gravatar for marcoalbuquerque.sfu
3.7 years ago by
marcoalbuquerque.sfu50 wrote:

First Question,

Where in the Galaxy file system are the parallelism modules defined? I.e. where can if learn how galaxy handles parallelism?

Second - Real - Question,

Given the following tag:

<parallelism method="multi" split_inputs="interval_file" split_mode="to_size" split_size="1" shared_inputs="normal,tumour,config" merge_outputs="snvs,indels"></parallelism>

How does galaxy handle multiple merge_outputs. I keep getting an error saying that galaxy is passing three inputs to my merge function I defined for VCF Files (which only takes two).

Shouldn't Galaxy be calling this function twice with the respected inputs accumulated for each subprocess? It seems like it is passing the following:

merge(split_inputs, ... ) where the ... is the values found in the tag set. THIS DOES NOT SEEM GOOD.

Should have the following:

merge(snvs_split_inputs, snvs_output) & merge(indels_split_inputs, indels_output)

Please help me with this, I require multiple outputs, and the parallelism works, except for this merge step.

parallelism galaxy tag • 873 views
ADD COMMENTlink modified 3.7 years ago by Jennifer Hillman Jackson25k • written 3.7 years ago by marcoalbuquerque.sfu50
gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


If I understand this correctly, the way to do this is to have functions you build up accept multiple inputs (>2) using a repeat block. There are a few tools that do this already, with some very simple examples being "Concatenate" (galaxy-dist / tools / filters / catWrapper.xml) and "VCFCombine" (

Hopefully this helps, Jen, Galaxy team


ADD COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson25k
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