Question: Running multiple workflows with multiple inputs
2
gravatar for balaszone
2.1 years ago by
balaszone60
balaszone60 wrote:

Hi,

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.

Bala

ADD COMMENTlink written 2.1 years ago by balaszone60
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