Currently, there isn’t an easy way to build mrs pipelines using tools from different packages. Nipype is a python library that lets you interface different MRI packages (such as fsl, spm, ants, anfi, freesurfer), a lot of popular bids apps use it to create their pipelines (fmriprep, mriqc, xcp_d). Nipype doesn’t include interfaces for mrs software though, but it’s possible to write new interfaces. I have written some interfaces for fsl mrs, mainly the basic preprocessing tools. It is possible to write interfaces for non-python packages, such as matlab (FID-A) and R (spant).
Having nipype interfaces for different mrs software could ease creating custom pipelines for mrs data. Here is the github repo, in case anyone is interested in writing new interfaces or using the existing ones.