Question: Running multiple workflows with multiple inputs
gravatar for balaszone
2.2 years ago by
balaszone60 wrote:


I recently learnt to create workflows and to script in galaxy using bioblend. Seems like a very useful method to automate the analysis. however, I'm trying to batch process workflow(s) with multiple inputs. i.e for example

Step 1: yields fastq files for 8 samples in an experiment. Each sample produces 8 outputs(fastq files). So in total there will be 8*8=64 files. Our Aim is to analyze each of those samples parallely. So need to send these sample outputs to next step of a workflow.

Step 2a: This concatenate tool should take 4 inputs(4 lanes of read1) of one sample and concatenate them to produce 1 output Step 2b: concatenate tool should take the other 4 inputs(4 lanes of read2) of the same sample and concatenate them.

Rest of the workflow process would be similar for each of the other samples.

I figured out the longest route to analyze this. That is After step 1, manually choose inputs for the next step in workflow for each sample and run it. But I want to automate everything. How would one go about doing this in API OR any other means?

Please advice.

Thanks in advance.


ADD COMMENTlink written 2.2 years ago by balaszone60
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