bamUtil | files provide some programs for working on SAM/BAM files | Genomics library

Thoughts on how to account for a pipeline which can use versions of a software which requires a (slightly) different shell call?

At times, switching between versions with conda, the shell calls are different, E.g. Samtools 0.1.18 and Samtools 1.3.1. require different formatting for a prefix.

I've thought of three ways, and am looking for additional suggestions:

1. I'll add a configuration variable in my YAML, use it to set the version number. Have a conditional such that only the matched version-rule is included. Similarly to the way I used a software choice flag here.

2. I'll do the version detection within the rule, and change the shell call accordingly. In the example above the only difference is the addition of a '-T' argument. This is simple, but I fear eventually I'll arrive at a situation where it is more than just an additional argument.

3. Write completely separate rules, with the version in the rule name, putting the onus on the user to pick the correct version. This will inevitable cause ambiguity conflicts, but I can handle those.

Reflection: I'm not convinced nesting conditionals is the best approach, as it makes maintenance more difficult, and it's really not that elegant. Having the detection in the rule isn't that bad, but I don't like the idea of the control flow being pushed into rules (right now it's all been removed from rules for my pipeline). I want to avoid creating ambiguity conflicts.

Am I missing supporting functionality? At first I thought it was this Snakemake's 'Version' directive, but it's not actually what I want. Either that or I'm missing how I am to utilize it.

Thoughts?

Samtools 1.3.1