New to running pipelines

[j-p-courneya]

Hi I have a goal of running the vector pipelines on some expt samples of my own and want to test out your WDL pipelines first on the data publicly available for this study.

Q1) I likely missed this but do I need to install Cromwell on my server to run these pipelines? Do you have instructions on setting this up to run? I am very happy to provide feedback on deploying these pipelines on my server.

Q2) why does the alignment WDL take bam as input? I don't understand this I thought that bams are output from alignment.

Q3) where do I access the reference genome for the analysis?

Thank you for making all your code available, the documentation provided and for taking time to respond to user inquiries.

JP