Hi,
I have a couple of GATK issues
1. First is there a data manager for it? I have tried Generate
GATK-sorted Picard indexes (data_manager_gatk_picard_index_builder) -
builder and got no entries on the cached picard genomes.
2. With problem 1, we are using genomes from the history. It so happens
that some XML files have the filtering of forcing the dbkey of
the from-history genome to be the same as the BAM files (reduced below
for easy reading):
<when value="history">
<param name="input_bam" type="data" format="bam"/>
<param name="ref_file" type="data" format="fasta">
<options>
<filter type="data_meta" key="dbkey" ref="input_bam" />
</options>
</param>
</when>
For example, here:
https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/gatk/realigner_target_creator/realigner_target_creator.xml#L69
Now, this does not seem to work. I.e. when I make the dbkey of the BAM
file and the FASTA file the same, the ref_file entry is still empty.
Also, some xml files have it, others do not.
As a temporary measure, I removed the options/filter in my local
installation, but might this be a bug? Or is it a bug in my head?
Thanks,
Tiago
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