I want to use GATK workflows such as seq-format-conversion on slurm. In order to apply the workflow on a pair of fastqs several parameters need to be defined in a json per file-pair. In the moment I am writing a rather clumsy R script doing that job and I wonder if there is a more elegant way scripting the generation of jsons for a batch of input files.
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.
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