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WatsonLab / MAGpy

Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
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Running a subset of jobs? #3

Closed adityabandla closed 5 years ago

adityabandla commented 6 years ago

Can a subset of jobs alone be run instead of all?

mw55309 commented 6 years ago

It depends what you mean.

To run everything on a subset of mags, just put fewer .fa files into the mags directory.

To run a different subset of the pipeline would require a bit of altering of the rule all, but it shouldn't be too hard....

adityabandla commented 6 years ago

Hi Mick

Apologies for the vague phrasing. I meant running a subset of the pipeline. I managed to figure out how to alter the snakemake pipeline

On another note, I think there is a bug in the rule definition for the phylophlan step. Once the output from Phylophlan is copied into the tree folder, the newick tree file still has the name of the process ID and not MAGpy.tree.nwk. So this throws a missing output file error

mw55309 commented 6 years ago

Thanks, will look into it :)