Good Morning,

We are also interested in this capability.  To give a concrete example,  we
sometimes receive multiple sequence runs 1Š*  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.

Is the galaxy team looking into these types of features or do other people
have custom solutions they are using?

Thanks so much,


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