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Implementing your workflows from git repository to run locally
First of all, thanks a lot for putting up those GATK workflows. As a non-bioinformatician at the core, I truly appreciate those shortcuts!
And this question comes right after I performed your first tutorial on workflows, and now I want to explore more of them.
I was particularly interested in starting by your "cnn-variant-filter", after reading about it here.
So, I pull the workflow and went straight to change its json file (
cram2filtered.inputs.json). First thing I notice is that all paths are set to
gs://. And second was that there are a lot of inputs that I don't know where to retrieve them. More specifically these lines:
"Cram2FilteredVcf.reference_fasta": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", "Cram2FilteredVcf.reference_dict": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dict", "Cram2FilteredVcf.reference_fasta_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", "Cram2FilteredVcf.resource_fofn": "gs://gatk-best-practices/cnn-h38/resource_fofn.txt", "Cram2FilteredVcf.resource_fofn_index": "gs://gatk-best-practices/cnn-h38/resource_fofn_index.txt", "Cram2FilteredVcf.calling_intervals": "gs://broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list"
Another thing is that the workflow is set to run by using a
.cram file as input. In my case, I would like to use
BAI as inputs.
That being said, how could I implement this to run locally and using BAM and BAI files as inputs? Would using the gatk docker help here? If so, how would I use it?
Any help is very much appreciated!