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Hi! I'd like to try this method (https://portal.firecloud.org/#methods/broadgdac/mutation_signature_analyzer/19) on some of my samples that I analyzed using the best practices Mutect2 workflow. I have some mafs from that that I want to analyze for mutational signatures, and I have just a couple questions about the method configuration. Below I provided the default configuration.
1) What is the "tumor_type" variable referring to? I just want to know what file in my workspace or bucket to specify.
2) I assume "maffile" is my maf that I want to be analyzed - do I specify the maf file by providing a "gs://" etc link to the bucket, or can I specify the maf by specifying the attribute as like "this.oncotated_m2_maf"