Question: I noticed that there is a file starting with double-underscore and ending in .mro that is generated in the parent directory where my 10x pipeline is run, i.e. __analysisName.mro, where analysisName corresponds to the
--id I specified for my analysis. What is this file?
Answer: 10x pipelines all operate using the Martian pipeline framework. Martian pipelines are defined by MRO files. When you run a 10x pipeline command (e.g.
cellranger count ...), you are executing a wrapper script whose purpose is to construct an MRO file that will run the pipeline according to the options you provide. This is the MRO file that you see. It is outside the analysis directory because it has to exist prior to running the analysis that creates that directory. Once the pipeline finishes, it is moved inside the analysis directory and renamed _invocation.
For extra information about MRO files and the Martian language please see: What is Martian?