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This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
modifying the processing-for-variant-discovery...inputs.json
Dear GATK Team,
I just successfully converted my fastq files to ubam and wanted to do a local data preprocessing using the uBAM to analysis-ready BAM universal pipeline.
I realized that I have to call the wdl file using the json file as an input.
I have some questions about editing the json file:
I. how should the flowcell_unmapped_bams_list be formatted? I have no access to the example "NA12878_24RG_small.txt"
II. I was able to download the “gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta” from the Resource Bundle under the Download section. Regarding the ones that end with human_g1k_v37_decoy.fasta.sa, amb, bwt, ann, pac. I was not able to find those in the Resource Bundle on the homepage.
III. I was able to place the paths for picard and gatk. But what is gotc? ("PreProcessingForVariantDiscovery_GATK4.gotc_path": "/usr/gitc/")
IV. There are options like GATK4.agg_small_disk, medium disk and large disk. Where do I choose that the program should run on a specific size?
V. I installed gatk locally using the gatkcondaev.yml without the need of docker? Can I run the whole pipeline without docker? The json file has some options called DOCKERS.
Thanks for your help