How do I write a script so I can use the same tool (I'm mostly using HaplotypeCaller and GenotypeGVCFs) on multiple sample files (I have 60 sample files) without having to run the same command for each sample file one by one and still have in the end a VCF file for each sample file?
I'm using GATK on Docker and I tried following the steps here: https://support.terra.bio/hc/en-us/articles/360037127992--1-howto-Write-your-first-WDL-script-running-GATK-HaplotypeCaller but I couldn't do it eventually and had error to access the wdltool.jar
I'm still new to command-line and coding so I'm not sure what to do exactly, and I haven't even understood fully the article I put above but I applied the steps exactly as written.
I appreciate your help.
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