search

WarrenLab / minigraph-cactus-nf

a nextflow pipeline for creating a pangenome with minigraph-cactus
GNU General Public License v3.0
13 stars 4 forks source link

Documented existing --scratch param in README.md. Exposed --jobStore … #1

Closed adadiehl closed 8 months ago

adadiehl commented 8 months ago

…argument to replace hard-coded ./jobStore. Added appropriate docs to README.md.

esrice commented 8 months ago

This looks good except that as it is now with no default for the --jobStore param, I think this will cause most of the steps to crash if it's not specified because cactus expects a jobstore location as a positional argument, so if it's left blank there will be one too few arguments into each cactus command. If you give it "./jobStore" as a default value I will merge.

I should also mark this repository as deprecated, though, because newer versions of cactus can run all of the commands in this pipeline with a single command, so there's not much use for a nextflow pipeline anymore.

adadiehl commented 8 months ago

Good point on the lack of a default value. That’s an easy fix.

 Having looked over the current MC pipeline, I have to say I prefer your nextflow implementation. The MC implementation seems heavily AWS-slanted and it wasn’t clear how readily it would translate to a local cluster environment. The nextflow approach is much cleaner in its implementation and has worked brilliantly with just a few minor tweaks for local cluster config. I personally think it's good to have another option!