I am playing with Galaxy "splitters" capabilities. After some cases that you help me out to solve I am facing a new issue, this is maybe due to my tool configuration file, but in any case I tell you what I've done.
What I would like to do exactly, is to split paired fastq, map them and then join them. This is my configuration file:
My problem of this configuration is that generates an empty file. So, after seeing the code, I discover that when it tries to join the several bam files it goes to the first parent: class Data( object ), to the method merge: def merge( split_files, output_file). So I may be wrong, but I think binary.bam class should override this method, is this right? if this is the case, I would like to implement this method, I have couple of basic ideas, like merge them with samtools. What do you think?
On ther other hand, is this related with the last email of John Chilton and the 15.03 release?
Functional Genomics Unit Bioinformatics and Genomics Department Prince Felipe Research Center (CIPF)
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at: