Good Morning,

We are also interested in this capability.  To give a concrete example,  we sometimes receive multiple sequence runs 1…*  for the same sample.  We would like to be able to process each run of the sample through BWA and then merge them together, post process it a bit, and then send the merged bam file through the rest of our standard pipeline.  

Ideally this would be automated.   Aurélien, I am interested in your workaround – this might get us part of the way there, as we could concatenate the fastq files together and run BWA once.  Would you be willing to share some of your custom tools for us to iterate on? But ideally, for performance, we would run the bwa steps in parallel.